A gas turbine engine fuel system including a combustor with at least one fuel injector, a fuel manifold that supplies fuel to each injector, a drain tank in fluid communication with the fuel manifold, and a vacuum generator that selectively provides below atmospheric pressure to the drain tank and includes first and second chambers separated by a flexible diaphragm. The fuel system also includes a first check valve that allows one-way flow from the fuel manifold into the fuel injector, and a second check valve that allows one-way flow from the fuel injector to the fuel manifold. The vacuum generator reduces a pressure within the second chamber causing the diaphragm to increase a volume of the first chamber and reduce a volume of the second chamber, such that expanding the first chamber causes below atmospheric pressure in the drain tank and fuel manifold, and the second check valve opens.