Systems and methods for compensating for nozzle coking in fuel injection system include creating expected fuel flow rate formula for selected fuel injection nozzle, operating selected fuel injection nozzle for a time, measuring fuel pressure and injector control valve on-time of fuel injection nozzle during operation, determining expected fuel flow rate for measured fuel pressure and injector control valve on-time, measuring actual fuel flow rate of fuel injection nozzle, determining coking condition of fuel injection nozzle, and automatically altering injector control valve on-time to compensate. Expected fuel flow rate formula is determined as function of fuel pressure and injector control valve on-time, while actual fuel flow rate is measured by flow rate sensor attached to injection system. Sometimes, coking condition determination is based on difference between actual fuel flow rate and expected flow rate. Compensation in control valve on-time is necessitated by deterioration in actual fuel flow to cylinder.