The long-term bit error rate (BER) performance of partial response maximum likelihood (PRML) system using an adaptive equalizer in a perpendicular magnetic recording (PMR) channel with thermal decay is studied. A thermal decay model based on the experimental data giving the amplitude change of reproducing waveforms with the elapsed time for CoPtCr-SiO2 PMR medium is obtained. The BER performance of PR1ML channel for the 16/17(0,6/6) run-length-limited (RLL) code is evaluated by computer simulation using the model. The relationship between the ratio RJ of the jitter-like media noise power to the total noise power at the reading point and the required SNR to achieve a BER of 10-4 is also obtained and the performance is compared with that of the conventional equalization. The results show that the significant improvement in SNR by utilizing the adaptive equalization is recognized over all RJ compared with the conventional equalization.