Femtosecond laser drilling induces PN junction in p-HgCdTe. In this work, femtosecond laser with repetition rate of 1 kHz was used to generate different micrometer-sized holes. It was found that the pulse number is an important parameter which influences the effect of junction formation. Laser beam induced current (LBIC) characterization shows that the inversion layer thickness reduces from 13.5 μm to 10.5 μm when the pulses increase from one to ten. The LBIC profile of a hole created with one hundred pulses deviates severely from the line shape of ideal PN junction, resulting in large leakage current. In addition, the fitting of LBIC curves shows that the diffusion length of the hole created by a single pulse is 17 μm whereas the one created by ten pulses reduces to 12 μm.