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The bed rail dimensions haven't changed since 1999. That's why for example I took a tonneau for a 2011+ and put it on my old 2002. It was a perfect fit.
However, in some cases there are tonneaus, caps, and canopies that extend downward over and in front of the tailgate. If yours is this style it's possible it could hit the newer tailgate. It's only a slight difference, but it can be a hassle to deal with.
However that's rare to happen, so most likely you are good to go. After all, many folks take their 99-07 trucks and swap to an 08+ tailgate without issues, even with existing covers and caps.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.