In order to dynamically align one or more printheads in a printer, a referencing mechanism is placed on the printer and a detector is placed on the printhead. The printhead is moved at a known speed past two spaced apart reference indicia of the referencing mechanism. The passing of a first of the spaced apart reference indicia is detected and the passing of a second of the spaced apart reference indicia is detected. The time between the detection of the first reference indicia passage and the detection of the second reference indicia passage is measured and a delay time, related to the measured period of time, is created. Energization of an ink drop ejection is delayed for the duration of the delay time.