The Navigator was updated in 2003, along with the Ford Expedition, on the new Ford U platform. The interior was also substantially revised to bring it up to the level expected by luxury buyers. Some ingenious features debuted with this redesign, including power-deployable running boards that deploy when a side door is opened, a power liftgate, and a power folding third row seat.

Tire-pressure monitoring was made standard for 2004, with Roll Stability Control an option, and the mid-level Premium trim line was deleted. Along with a light facelift the powertrain was revised for 2005, with the DOHC 5.4 L V8 being replaced by a new SOHC 3-valve design borrowed from the F-150, driving the wheels through a new ZF Friedrichshafen AG-sourced 6-speed automatic transmission. The stability system was now standard on all models. An Elite package for the Ultimate trim includes a THX audio system, rear-seat entertainment, and HID headlights for 2006, the last year of this generation.