Where is the fuel filter located on a 1999 Ford Mustang? It is an in-line fuel filter located behind the rear bumper. It's a steel line that will have a module connected to it. Basically, the fuel filter itself is in the 1999 Ford Mustang Fuel Filter Replacement | CarParts Get the best deal for a 1999 Ford Mustang Fuel Filter. Fast shipping with low price guarantee. Order online today!