A system for compensating for heat induced transient phase shift in a heat assisted magnetic recording system. A heat assisted magnetic data recording system includes a near field thermal transducer that locally heats the media during writing. The thermal transducer, when activated, results in a change in size of a magnetic transition written to the magnetic media. This change in size of the thermal transition results in a transient phase shift of the data recorded on the magnetic media. The system includes circuitry for predetermining an anticipated amount of transient phase shift and adjusting a subsequent read signal to compensate for the known transient phase shift, thereby eliminating signal errors resulting from the transient phase shift.