System and method for learning an injector compensation

A method of operating a fuel injector includes determining a fuel pressure and a total fuel mass MTF to be injected per combustion cycle, defining first and second pulse widths PW1 and PW2 corresponding to first and second commanded fuel masses CM1 and CM2 wherein CM1+CM2=MTF, actuating the injector for the first and second pulse widths, detecting an opening delay for the injector, and storing the opening delay. The method may further include increasing PW1 and decreasing PW2 by a predetermined amount, repeating selected steps until PW2 is less than or equal to a predetermined minimum pulse width, changing the fuel pressure by a predetermined pressure amount, cycling through selected steps until the fuel pressure reaches a predetermined target fuel pressure, and commanding the injector to open earlier than a normally commanded opening time by a lead time based on stored opening delay data.