Purpose In segmented ART treatment or so-called 'freeze-all' strategy fresh embryo transfer is deferred, embryos cryopreserved, and the embryo transferred in a subsequent frozen embryo transfer (FET) cycle. The purpose of this cohort study was to compare a GnRHa depot with an oral contraceptive pill (OCP) programming protocol for the scheduling of an artificial cycle FET (AC-FET) after oocyte pick-up (OPU). Methods This retrospective cohort study was conducted on prospectively performed segmented ART cycles performed between September 2014 and April 2015. The pregnancy, treatment duration, and cycle cancellation outcomes of 170 OCP programmed AC-FET cycles were compared with 241 GnRHa depot programmed AC-FET cycles. Results No significant difference was observed in the per transfer pregnancy and clinical pregnancy rates between the OCP and GnRHa groups, 72.0 versus 77.2 %, and 57.8 versus 64.3 %, respectively. Furthermore, the early pregnancy loss rate was non-significantly different between the OCP and GnRH protocol groups, 19.8 versus 16.7 %, respectively. However, nine (5.29 %) cycles were cancelled due to high progesterone in the OCP protocol group, while no cycles were cancelled in the GnRHa protocol group and the time taken between OPU and FET was 19 days longer (54.7 vs 35.6 days) in the OCP protocol compared to the GnRHa protocol. Conclusions The results of this AC-FET programming study suggests that the inclusion of GnRHa depot cycle programming into a segmented ART treatment will ensure pregnancy, while significantly reducing treatment duration and cycle cancellation.