A method for measuring noise of a magnetic head includes setting a plurality of threshold values, applying bias current or voltage to a read element of the magnetic head, applying an external transverse magnetic field to the magnetic head, amplifying output signal from the read element to produce an amplified signal, filtering the amplified signal to produce a filtered signal, generating an enable signal for each threshold value in a predetermined time window by a counting control means with input signals which include the filtered signal and the threshold value, measuring the cumulative time duration of each enable signal, making an amplitude-duration distribution according to the cumulative time durations and the threshold values, calculating a plurality of parameters according to the amplitude-duration distribution and analyzing the parameters with a plurality of predetermined criteria to determine the defects of the magnetic head. Accordingly, the invention also discloses a system for measuring noise of a magnetic head.