A system and method for real-time, self-learning characterization of fuel injector performance during engine operation. The system includes an algorithm for an engine controller which allows the controller to learn the correlation between the fuel mass and pulse width for each injector in the engine in real time while the engine is running. The controller progressively perceives those pulse widths that achieve the desired fuel mass, while it can continuously adapt what it has learned based on various input variations, such as temperature and fuel rail pressure. The controller then uses the learned actual performance of each injector to command the pulse width required to achieve the desired quantity of fuel for each cylinder on each cycle.