One problem related to accelerator pedal has been reported for the 1999 Lincoln Navigator. The most recently reported issues are listed below.
Ongoing problem with engine stalling when applying accelerator pedal from a stop position or while starting vehicle and shifting into drive. Vehicle been into dealer shop on four occasions, and unable to locate cause.
| Cruise Control problems | |
| Vehicle Speed Control problems | |
| Speed Control Linkage problems | |
| Accelerator Pedal problems |