Lincoln Navigator Transmission Problems & Cost | 4R100 / 6R80

The Lincoln Navigator was equipped with the 4R100 (or E4OD) in early models and 6R80 in later models. But they aren’t without their problems though, so let’s look at some of the most common Lincoln Navigator transmission problems, look at cost estimates and figure out what you can do about them.

Need a replacement transmission? Get an estimate for replacement transmissions and local installation. Look up your transmission model by vehicle make and model.

What Transmission Do I Have?

Lincoln Navigator Transmission Models

Lincoln Navigator: 4R100 Transmission (1998 – 2008)
Lincoln Navigator: 6R80 Transmission (2009+)

Lincoln Navigator Transmission Replacement Cost Estimate

Pricing varies by model. To be 100% sure on pricing, have your VIN# handy and use our Get An Estimate feature to look up your transmission by VIN#.

Replacement Lincoln Navigator Transmission Prices:

What are the DTC codes related to Lincoln Navigator transmission problems?

Lincoln Navigator Transmission Recalls

Recall ID 12C23-S1 – Ford 6R80 Transmission

– Summary
In May 2012, the Ford Motor Company issued a compliance recall on the following vehicles equipped with the 6R80 transmission:

2011 – 2013 Ford F150
2011 – 2013 Ford Expedition
2011 – 2013 Ford Mustang
2011 – 2013 Lincoln Navigator

– Consequence
It seems that a faulty 6R80 transmission range sensor / TRS can cause a number of transmission problems when the shifter is placed in the Reverse position. The symptoms include failure to engage reverse gear, the electronic PRNDL indicator will not display reverse (if equipped), the backup lamps will not function, and intermittent rear video camera operation (if equipped).

– Remedy
Replace the 6R80 transmission lead frame (which includes the TRS sensor). Owners may contact Ford at 1-866-436-7332 or NHTSA at 1-888-327-4236

Lincoln Navigator Technical Service Bulletins (TSB)

TSB 02–21–1 – 4R100 Transmission – Torque converter access plug may become dislodged
1989 – 1997 Ford Super Duty – 1989 – 1998 Ford F250 – 1989 – 1998 Ford F53 Motorhome – 1989 – 2003 Ford E-Series – 1989 – 2003 Ford F150 – 1999 – 2003 Ford Super Duty – 2000 – 2003 Ford Excursion – 1998 – 2003 Lincoln Navigator – 2002 – 2003 Lincoln Blackwood
Problem – Due to extreme load and material shrinkage, the torque converter external access dust plug may fall out during severe duty use.
Solution – Install new plug (part number E9TZ-7N171-A) with a 1/4 inch bead of silicone sealant around the plug.

TSB 98-20-9 – Ticking noise on initial startup when the selector is in park or neutral – 4R100 Transmission
1998 Ford Econoline – 1998 Ford Expedition – 1998 Ford F150 – 1998 Ford F250 – 1998 Lincoln Navigator – 1999 Ford F250 HD – 1999 Ford F350 – 1999 Ford Super Duty
Problem – A ticking noise may be hard when the vehicle is first started and the shifter is in the ‘P’ or ‘N’ position. In some cases, the noise may also be heard after the vehicle has warmed up. This can be caused by the overdrive clutch steel separator plate(s) hitting against the case internal spline.
Solution – Install new OD friction plates and accumulator assembly

TSB 10-18-1 – Delayed forward/reverse engagement after cold starts – 6R80 transmission
2007 – 2010 Ford Expedition – 2009 – 2010 Ford F150 – 2009 – 2010 Lincoln Navigator
Problem – Some vehicles equipped with the 5.4L engine and the 6R75 or 6R80 transmission may experience delayed forward and/or reverse engagement after a cold start or in cold climates. The P0741, P0731 and/or P0735 DTC’s may also be present.
Solution – A new front pump adapter seal and separator plate will need to be installed. The main oil pressure regulator valve and its bore may also need to be cleaned.

TSB 11-8-4 – Fluid leak from bell housing – 6R80 transmission
2011 Ford Expedition – 2011 Ford F150 – 2012 Ford Mustang – 2011 Lincoln Navigator
Problem – Some vehicles built between 4/15/2011-6/8/2011 may experience a transmission fluid leak coming from the bell housing area.
Solution – Install updated transmission pump assembly

TSB 14-0217 – Delayed engagement park forward or reverse
2011 – 2014 Ford Expedition – 2011 – 2014 Ford F150 – 2011 – 2014 Ford Mustang – 2011 – 2014 Lincoln Navigator
Problem – Some vehicles may experience a noticeable delay when trying to engage a forward or reverse gear from Park. This can happen with the vehicle is cold (i.e. has not been driven for several hours).
Solution – Install updated 6R80 transmission pump

TSB 18-2079 – Harsh or delayed shifting and/or P0711 DTC – 10R80 Transmission
Problem – Some owners may experience usually harsh or delayed gear changes. There may also be a P0711 diagnostic trouble code saved in the transmission control module
Solution – The powertrain control module will need to be updated with new software (release 108.04 or higher). Once the update is complete, the adaptive transmission shift strategy program may temporarily cause usually firm upshifts and downshifts while it ”relearns” your driving style.

Common Lincoln Navigator Transmission Problems

TCC Application in 2nd Gear – 4R75E Transmission / 4R70 Transmission
Problem – A lack of power after the 1-2 shift can be caused by an un-commanded torque converter clutch application / TCC apply. The P0742 and/or P1742 DTCs may also be stored.
Solution – The #7 check ball inside of the valve body may have worn down to an incorrect size, allowing the torque converter clutch to apply after the 1-2 shift. Replacement of this check ball may solve the problem.

Slipping in All Forward Gears – 4R75E Transmission
Problem – Many 2005 – 2006 Ford vehicles equipped with the 4R75E transmission, may experience excessive slipping in all forward gears. Metal shavings may also be present in the transmission fluid.
Solution – Replace forward clutch drum and update ECU with program 06B06

Poor performance with DTCs P0715, P0716 & P0717 – 4R100 Transmission
Problem – Poor engine performance and acceleration may be due to a sticking solenoid regulator valve
Solution – If the solenoid regulator valve cannot be repaired, the valve body will have to be replaced

Lack of Response
Leaking Fluid
Low Fluid
Burning Smell
Grinding or Shaking
Whining, Clunking or Humming
Refuses to Go Into Gear
Torque Converter Issues
Valve Body Issues
Transmission Noisy in Neutral
Gears Slipping
No 3rd or 4th Gear
No 1st or 2nd Gear
No Reverse
Dragging Clutch
Trouble Codes / Check Engine Light

Can I drive with a transmission problem?

If your Lincoln Navigator can still make it up and down the road, you might say “It’s fine, I’ll just drive it until I can get it fixed”. But that is not always a good idea, depending on the symptoms. You see, there are a lot of (very expensive) moving parts inside of a transmission, and if something isn’t right, continuing to drive with a transmission problem could damage something else.

How often does a Lincoln Navigator transmission need to be replaced?

The overall lifespan of a Lincoln Navigator transmission largely depends on how well it was maintained. Factory design flaws also factor into this equation, along with how/how hard you drive. But on average, we’ve seen the Lincoln Navigator transmission last for between 130,000-180,000 miles. A high quality replacement transmission however, can last considerably longer if all of the factory design flaws have been addressed and the vehicle has been maintained.

How are Lincoln Navigator transmission issues diagnosed?

It is fairly easy to guesstimate what the root cause of your Lincoln Navigator transmission problems might be, but you won’t truly know unless you have the right tools and experience. A good mechanic or transmission repair center will be able to connect your truck to a computer and find out which diagnostic trouble codes (DTC’s) have been stored. Once they know what to look for, they can perform a visual inspection to verify the problem.

How is a Lincoln Navigator transmission replaced?

In order to replace your Lincoln Navigator transmission, the truck has to be lifted from the ground in order to gain access to all of the parts that will need to be unbolted. Then the transmission can be lowered to the ground (typically with a transmission jack), so the new transmission can be installed. Once it is in place, for the 6L80, the vehicle PCM will have to be reprogrammed / reflashed to accept the new transmission using the latest GM subscription.

Recommendations for Lincoln Navigator transmission issues?

To save time and get back on the road faster, have your 17-digit truck VIN# handy and you can get an online quote for a reman Lincoln Navigator transmission here, then find a local shop using our Find a Shop guide to install it for you.

How to Solve Lincoln Navigator Transmission Problems

Solution A: Buy a Used Lincoln Navigator Transmission

The quickest way to fix your transmission problems is to simply buy a used transmission or used transmission. These can be found at most junk yards, and they often come with a 30-90 day warranty. However, there’s no way to determine the actual condition of the internal components, so you could be spending a bunch of money to have the exact same problems. Plus, that warranty only covers the transmission if it’s defective, not the labor costs that you’ll have to pay.

Solution B: Buy a Rebuilt Lincoln Navigator Transmission

Another option would be a rebuilt transmission or rebuilt transmission. A local repair shop will remove your transmission, then install a bunch of new parts during the rebuild. The problem here is, the skills and experience of each transmission rebuilder will vary widely from shop to shop, so you could have problems from something that wasn’t adjusted properly. And the 1-2 year warranty might only cover you at certain transmission repair shops, in a specific geographical area.

Solution C: Buy a Remanufactured Lincoln Navigator Transmission

Many owners depend on their vehicle to commute and get things done. Their gasoline engines are designed to go 100’s of thousands of miles, so it makes sense to invest in a remanufactured transmission.

Need a replacement transmission? Get an estimate for replacement transmissions and local installation. Look up your transmission model by vehicle make and model.

What Transmission Do I Have?

What Problem Does Your Lincoln Navigator Have?

Let us know the year, mileage and problem you’re having as well as any trouble (OBD) codes you’ve found. If you’ve been given a quote or paid for a repair, we’d like to hear about that too!