A by-pass fuel system in which the plumbing of the fuel pump module is configured to ensure by-pass strained (and filtered) fuel remains separate from the reservoir fuel after by-pass such that it is not re-strained before re-entry to the fuel pump. The anti-clogging fuel pump module is plumbed such that the by-pass strained fuel is directed to the fuel pump separately with respect to the reservoir fuel, wherein it never mixes with reservoir fuel except after the reservoir fuel has passed through the strainer. Thus, the by-pass strained fuel only mixes with strained fuel from the strainer before its entry to the fuel pump. Accordingly, only reservoir fuel in the fuel pump module is passed through the strainer, whereby the clogging rate of the strainer is minimized.