We report on the detection of a pulsating Fe Ka line in the High Mass X-ray Binary (HMXB) GX 301-2, from a 40-ks Chandra observation near periastron. The pulsations in the Fe Ka emission appeared only in the first 7 ks of the observation, with a period and phase profile similar to those of the continuum. The presence of pulsed fluorescent lines is an unusual property in HMXBs. After 7 ks, the continuum flux increased by a factor of three, the Fe Ka flux increased only by about 10%, and the pulsating signal in the line disappeared. Finally, in the second half of the observation, both the continuum and the line flux dropped by a similar factor of 2. We suggest that the pulsating component of the Fe Ka line is coming from a transient non-isotropic distribution of dense gas around the neutron star, for example an accretion stream induced by periastron passage, or from the illuminated surface of the donor star.