2016 Honda Pilot Problems

If you own or are considering a 2016 Honda Pilot, you’re likely aware of its reputation for reliability and family-friendly utility. However, like any vehicle, it has its share of known problems. Understanding these 2016 Honda Pilot problems can save you time, money, and frustration down the road.

This guide will walk you through the most common issues reported by owners and mechanics. We’ll provide clear explanations of the symptoms, potential causes, and practical fixes. Our goal is to give you the knowledge you need to address these problems confidently, whether you’re tackling them yourself or discussing them with a technician.

The 2016 model year was the first of the third-generation Pilot, and it introduced a new 3.5-liter V6 engine with direct injection and a new 9-speed automatic transmission (9AT) on higher trims. While a great SUV overall, several patterns of issues have emerged. The most frequent complaints center around the transmission, electrical systems, and some engine-related concerns.

1. Transmission Shuddering and Jerking

This is arguably the most reported issue for the 2016 Pilot, especially in models equipped with the 9-speed automatic transmission. Owners describe a pronounced shudder or jerking sensation, typically during light acceleration or when cruising at highway speeds between 40-60 mph.

It often feels like driving over rumble strips. This problem is not only annoying but can lead to premature wear on transmission components if left unaddressed.

Symptoms: Violent shaking or shuddering during light throttle input, hesitation when accelerating, rough shifts, the feeling of the transmission “hunting” for the right gear.
Primary Cause: The issue is frequently traced to the torque converter. The lock-up clutch inside the torque converter can engage and disengage erratically, causing the shudder. Low transmission fluid level or degraded fluid can also contribute.
Potential Fixes:

Software Update (TCM Reprogramming): Honda has issued Technical Service Bulletins (TSBs) for this. A dealer can reprogram the Transmission Control Module (TCM) with updated software to smooth out the torque converter lock-up strategy. This is often the first and most effective step.
Transmission Fluid Change: A drain and refill with Honda-approved ATF (often ATF DW-1) can sometimes help, especially if the fluid is old or contaminated. Avoid a “flush” which can cause problems; a simple drain and fill is safer.
Torque Converter Replacement: If the shudder persists after a software update and fluid change, the torque converter itself may be faulty and require replacement. This is a more involved and expensive repair.

2. Electrical Gremlins and Battery Drain

The 2016 Pilot has a suite of advanced electronics, and some systems have proven problematic. A common complaint is unexplained battery drain, leaving owners with a dead battery after the car sits for a short period.

Other electrical issues involve flickering dashboard lights or malfunctioning infotainment screens.

Symptoms: Dead battery overnight, frequent need for jump-starts, flickering interior lights, the infotainment system freezing or rebooting randomly, power tailgate acting erratic.
Primary Cause: Parasitic drain is the main culprit for battery issues. A module or component fails to go to “sleep” when the vehicle is off, slowly draining the battery. Faulty software in the audio/navigation unit or a bad relay are common sources.
Potential Fixes:

Battery Test & Parasitic Draw Test: First, have the battery tested to rule out a bad cell. Then, a technician should perform a parasitic draw test to identify which circuit is pulling power while the car is off.
Software Update for Audio Unit: Honda has TSBs for audio system software updates that can resolve freezing and battery drain related to the infotainment system.
Inspect and Replace Faulty Relays: The accessory power socket relay (often in the under-hood fuse box) is a known failure point that causes drain. Replacing it is a cheap and simple fix if it’s the problem.

3. VCM Engine Vibrations and Oil Consumption

The 2016 Pilot’s 3.5L engine uses Honda’s Variable Cylinder Management (VCM) system. It deactivates three cylinders during cruising to save fuel. While the technology is sound, its implementation can cause issues over time.

Excessive vibration when VCM is active is a common complaint. Some owners also report higher-than-normal oil consumption between changes.

Symptoms: Rough idle, excessive vibration felt in the steering wheel and seats during highway cruising, the “ECO” light staying on constantly, needing to add oil between scheduled oil changes.
Primary Cause: Vibration is often caused by worn engine mounts, which deteriorate faster due to the uneven firing pulses from VCM. Oil consumption can be related to VCM causing piston ring wear or carbon buildup on valves due to the direct injection system.
Potential Fixes:

Install a VCM Disabler (Tuner): Many owners opt for aftermarket devices that prevent the VCM system from activating. This eliminates the vibration at its source and may reduce long-term wear. It’s a popular and effective mod.
Replace Engine Mounts: Upgrading to newer, revised engine mounts or aftermarket mounts designed to handle VCM vibrations can significantly smooth out the ride.
Monitor Oil & Use Top-Tier Fuel: Check your oil level regularly between changes. Using high-quality Top Tier gasoline can help reduce carbon buildup on intake valves, a common issue with direct injection engines.

4. Power Tailgate Malfunctions

The automatic power tailgate is a convenient feature, but it’s another source of headaches for some 2016 Pilot owners. Problems range from the tailgate not opening or closing fully to it reversing direction for no apparent reason.

It can sometimes beep repeatedly or just stop working altogether.

Symptoms: Tailgate beeps multiple times and won’t open/close, reverses direction mid-cycle, only opens partway, or is completely inoperative from all switches (key fob, dashboard, tailgate button).
Primary Cause: The most common cause is a failure of the tailgate’s internal hydraulic strut or its position sensor. Water intrusion into the power tailgate motor or control unit can also cause failure. Sometimes, its just a simple misalignment.
Potential Fixes:

Manual Reset Procedure: Often, you can reset the system by manually opening the tailgate to its full height, holding the close button for 5 seconds until it beeps, then manually closing it. Consult your owner’s manual for the exact procedure.
Check for Obstructions and Alignment: Ensure the tailgate is properly aligned and that the rubber seals are clean. Even a small obstruction in the latch can cause it to reverse.
Replace the Power Strut Assembly: If resetting doesn’t work, the power strut is likely faulty. Replacing the entire strut assembly (motor and strut combined) is the typical repair.

5. Premature Brake Wear and Rotor Warping

Many 2016 Pilot owners report needing to replace brake pads and rotors much sooner than expected—sometimes before 30,000 miles. Warped front rotors that cause steering wheel vibration during braking is a particularly frequent complaint.

This issue can effect the driving feel and safety of the vehicle.

Symptoms: Pulsation or vibration in the steering wheel when applying the brakes, squealing or grinding noises, a need for frequent brake service.
Primary Cause: The factory-installed brake rotors on some Pilots seem prone to warping under heat stress. Aggressive driving, towing, or simply the weight of the SUV can contribute. Using lower-quality replacement parts can also lead to a quick return of the problem.
Potential Fixes:

Upgrade to High-Quality Rotors: When replacing, choose high-quality, coated or slotted rotors that better dissipate heat. Avoid the cheapest options.
Use Ceramic or Semi-Metallic Pads: Pair the new rotors with a reputable brand of ceramic brake pads, which tend to produce less dust and are easier on rotors than some semi-metallic pads.
Proper Bedding-In Procedure: After new pads and rotors are installed, follow a proper bedding-in procedure. This involves a series of moderate stops to transfer pad material evenly onto the rotor, which helps prevent warping and ensures optimal performance.

6. Air Conditioning (A/C) Failure

A less common but serious issue is complete A/C failure. Owners report the system blowing warm air suddenly, often on the driver’s side first (due to the dual-zone system).

Repairs for this can be expensive, as the cause is often a major component failure.

Symptoms: Warm air from vents, A/C clutch not engaging, hissing noise from the dashboard (indicating a leak), reduced cooling performance.
Primary Cause: The most prevalent cause for catastrophic failure is a cracked or leaking condenser. Road debris can damage it. Other causes include a failed compressor, expansion valve, or leaks in the evaporator core inside the dashboard.
Potential Fixes:

Leak Test and Diagnosis: A professional must perform a leak test with UV dye to locate the source of the refrigerant leak. This is not a DIY-friendly diagnosis.
Condenser Replacement: If the condenser is leaking, it must be replaced. Honda has a warranty extension for the condenser on some models, so check with a dealer first—you might be covered.
Full System Repair: If the compressor has failed, it often sends metal debris throughout the system. This requires replacing the compressor, condenser, receiver/drier, and flushing the lines—a very costly repair.

Proactive Maintenance Tips for Your 2016 Pilot

Beyond addressing specific problems, staying on top of maintenance can prevent many issues.

Transmission Fluid: Change it more frequently than Honda’s “lifetime” recommendation. Every 30,000-40,000 miles is a good practice for the 9AT.
Battery Health: Have your battery and charging system tested annually, especially before winter. Clean the terminals to prevent corrosion.
Use the Right Oil: Always use the recommended 0W-20 synthetic oil. Regular changes are crucial for VCM engines.
Listen for Noises: Pay attention to new sounds like creaks from the suspension, whines from the transmission, or clicks from the CV joints.
Check for TSBs and Recalls: Regularly visit the NHTSA website or ask your dealer to check your VIN for any open Technical Service Bulletins or recalls related to your Pilot.

Is the 2016 Honda Pilot Still a Good Buy?

Despite these common problems, the 2016 Honda Pilot remains a strong contender in the used three-row SUV market. Its spacious interior, comfortable ride, and strong resale value are big pluses.

When shopping for one, a thorough pre-purchase inspection by a trusted mechanic is essential. Look for service records that show proactive maintenance, especially transmission fluid changes. Consider opting for a lower trim with the older but more reliable 6-speed automatic transmission if you want to avoid the 9AT shudder issues entirely.

Being aware of these potential problems puts you in the driver’s seat. You can either budget for potential repairs or seek out a model that has already had them addressed. With the right care and attention, your 2016 Pilot can provide many more miles of reliable service for you and your family.

Frequently Asked Questions (FAQ)

What is the most serious problem with the 2016 Honda Pilot?
The transmission shudder issue is the most widespread and concerning, as it effects drivability and can lead to costly repairs if the torque converter fails. Electrical drain problems are also serious as they can strand you with a dead battery.

Are there any recalls on the 2016 Honda Pilot?
Yes. Recalls have included issues like faulty fuel pumps, missing side-view mirror welds, and software updates for various systems. Always check the NHTSA website with your VIN for the most current recall information.

How long will a 2016 Honda Pilot last?
With proper maintenance and timely repairs for known issues, a 2016 Pilot can easily last 200,000 miles or more. Honda’s J-series V6 engine is known for its longevity when cared for.

Is it expensive to maintain a 2016 Pilot?
Routine maintenance costs are average for the class. However, repairs for the transmission, A/C system, or power tailgate can be expensive, often exceeding $1,000. Staying proactive with fluid changes is key to avoiding big bills.

Should I avoid the 9-speed automatic transmission?
Not necessarily, but you should be cautious. Test drive the vehicle extensively at various speeds and listen for shuddering. A vehicle with a documented TCM update and recent transmission fluid service is a better bet. The 6-speed automatic is generally considered more robust.