2016 Honda Pilot: The Most Common Problem and How Owners Are Dealing With It

The most commonly reported problem on the 2016 Honda Pilot is transmission hesitation and rough/jerky shifting, especially on models equipped with the 9‑speed automatic, though some 6‑speed units also exhibit sluggish or abrupt gear changes. Owners frequently describe a lag pulling away from a stop, gear “hunting” at low speeds, and occasional hard upshifts or downshifts; software updates and fresh transmission fluid often help, but some vehicles require deeper diagnosis or component repair. This article explains how the issue presents, why it’s so prevalent on this model year, and the practical steps owners can take to address it.

Why transmission issues top the complaint lists

The third‑generation Pilot (2016 model year launch) introduced new powertrain combinations: a 6‑speed automatic in lower trims and a then-new 9‑speed automatic in higher trims. Early calibration quirks, adaptive shift learning that didn’t suit all driving patterns, and sensitivity to fluid condition contributed to widespread reports of hesitation, gear hunting, and abrupt shift quality. Complaint databases and owner forums consistently show these drivability concerns as the leading issue for the 2016 Pilot.

Which trims are most affected

While both transmissions appear in owner complaints, the 9‑speed automatic used on Touring and Elite trims draws the bulk of reports for hesitation and jerky shifting, particularly at low speeds or during rolling stops. LX, EX, and EX‑L models with the 6‑speed can also exhibit sluggish response or a mild shudder, though typically at lower frequency and severity compared with the 9‑speed units.

How the problem shows up in daily driving

Drivers tend to notice the issue in predictable situations. These symptoms can vary from mild to disruptive depending on calibration version, driving style, and vehicle maintenance history.

• Noticeable lag when accelerating from a stop, as if the vehicle “thinks” before engaging a gear
• Gear hunting or indecisive shifting at 15–45 mph, especially in light throttle city driving
• Abrupt or harsh upshifts/downshifts, sometimes felt as a jolt
• Low‑speed surging or a brief shudder when the torque converter locks/unlocks
• In 9‑speed models, awkward transitions around the auto idle‑stop re‑engagement

If you consistently experience these behaviors—particularly after the vehicle has warmed up—it’s worth having a dealer check for software updates and to evaluate fluid condition and any stored diagnostic data.

What Honda has done about it

Honda has issued multiple service updates over the years aimed at smoothing shift logic and torque converter behavior. Dealers commonly perform transmission control module (and, when applicable, engine control) software updates, run adaptive shift relearn procedures, and replace aging fluid with the latest specified automatic transmission fluid. In a subset of cases, additional repairs—such as replacement of certain transmission control components or, rarely, internal transmission repairs—have been performed under warranty when updates did not resolve the concern.

What owners can do right now

Tackling the issue typically starts with verifying the vehicle’s software and maintenance status, then escalating as needed based on symptoms and test results. The steps below can help you work methodically with a dealer or qualified independent shop.

1. Check your VIN for open recalls and service campaigns, and ask the dealer to confirm the latest transmission and powertrain software versions are installed.
2. Request a transmission fluid drain-and-fill with the current Honda-specified ATF if the fluid is old, contaminated, or past service intervals; confirm the correct fluid type is used for your transmission.
3. Have the shop perform the adaptive shift relearn procedure after updates or fluid service so the transmission can recalibrate to current conditions.
4. Document symptoms with specifics—speeds, throttle input, temperatures, and whether idle‑stop was active—to aid diagnosis and reproduce the concern on a road test.
5. If problems persist, ask for a deeper diagnostic including scan tool data (shift times, gear command vs. actual, torque converter slip) and check for applicable technical service bulletins.
6. For 9‑speed models, discuss idle‑stop behavior; some owners find disabling idle‑stop on short trips reduces awkward low‑speed transitions.
7. If the vehicle is under warranty or a goodwill consideration window, escalate through the dealer’s service manager and Honda customer care with your service history and diagnostics.

Many owners report meaningful improvement from software updates and fresh fluid alone. If those steps don’t help, thorough data‑driven diagnostics are key to identifying whether hardware repair is justified.

Other 2016 Pilot issues worth watching

While transmission complaints are the most common, a handful of other issues appear regularly in owner reports and service bays. Being aware of these can help you catch problems early.

• Air conditioning performance loss (often traced to leaks in the A/C system, including the condenser or lines)
• Infotainment glitches or freezing requiring system resets
• Brake vibration under light-to-moderate braking due to front rotor warping
• Intermittent battery drain or weak battery symptoms in vehicles driven mostly on short trips

These problems are not as prevalent as the transmission concerns but are common enough that a pre‑purchase inspection or proactive maintenance check is advisable, especially on higher‑mileage examples.

Summary

For the 2016 Honda Pilot, the most common problem is transmission hesitation and rough or jerky shifting—most frequently on 9‑speed models, but sometimes on 6‑speed versions as well. Honda’s remedies have centered on updated software, transmission relearn procedures, and fresh fluid, with additional repairs when warranted. If you’re experiencing these symptoms, verify software and fluid status first, document the conditions under which the issues occur, and work with a dealer or qualified technician to pursue the appropriate updates and diagnostics.

How many miles should a 2016 Honda Pilot last?

between 200,000 and 300,000 miles
Most well-maintained Honda Pilots last between 200,000 and 300,000 miles, which is significantly higher than the average vehicle lifespan in the U.S., typically around 150,000 miles. Here’s what that means in years: If you drive 15,000 miles a year, your Honda Pilot could likely last you 15 to 20 years or more.

What is the engine problem on the 2016 Honda Pilot?

The 2016 Honda Pilot has experienced several engine-related issues, including a significant recall for connecting rod bearing failure and subsequent engine seizure. Additionally, investigations and owner complaints point to other potential problems like engine misfires, stalling, and issues with the auto start/stop system. 
Engine Failure (Recall): A recall was issued due to a defect in the connecting rod bearing that can lead to engine failure while driving. This issue, initially affecting specific VINs, has also been reported in vehicles outside the recall scope. The repair can be costly, potentially ranging from $8,900 to $10,900. 
Engine Misfires and Fuel Delivery: Some 2016 Pilots have experienced engine misfires, potentially caused by debris from the high-pressure fuel pump or fuel injector machining process. This can lead to check engine lights, rough idling, and potential damage to the catalytic converter if not addressed. 
This video discusses engine misfires and potential fuel delivery problems: 59sLucore Auto and LucoreRacingYouTube · Feb 19, 2025
Auto Start/Stop System Issues: The auto start/stop system, designed to improve fuel economy by shutting off the engine at idle, has been a point of concern. Some owners reported the engine failing to restart, leaving them stranded. CNET reports that the National Highway Traffic Safety Administration (NHTSA) investigated these issues, along with similar problems in other Honda models with the same powertrain. 
Other Potential Problems:

• Stalling: Some owners have reported engine stalling, which can be a safety concern. 
• Excessive Oil Consumption: Some owners have reported excessive oil consumption. 
• Head Gasket Issues: In some cases, overheating due to potential head gasket issues has been reported, along with AC problems. 

This video shares insights from an owner who experienced various issues with their 2016 Honda Pilot: 1mAdventure Gear TVYouTube · Aug 18, 2024
Recommendation:
Owners of 2016 Honda Pilots should be aware of these potential engine issues and consider having their vehicles inspected, especially if experiencing any of the symptoms mentioned. If the vehicle is within the recall range, it’s crucial to address the connecting rod bearing issue promptly. For vehicles outside the recall, monitoring for signs of misfires, stalling, or other engine problems is recommended.

Is 2016 a bad year for Honda Pilots?

Honda Pilot Model Years With the Most Problems
Transmission problems were reported in 2005 Honda Pilots as well. The 2016 model year Pilot drew a high number of owner complaints related to the transmission, the engine, and the vehicle’s electrical systems.

What is the lawsuit on the 2016 Honda Pilot?

Moore v. Honda alleges that Honda vehicle models equipped with 9-speed transmission are at risk of experiencing symptoms of a transmission defect. Affected vehicle models include: 2016–2022 Honda Pilot, 2018–2019 Honda Odyssey, 2019–2025 Honda Passport and 2020–2025 Honda Ridgeline.