To compare the pregnancy rates of two methods of intrauterine insemination (IUI), i.e. standard IUI (sIUI) and fallopian tube sperm perfusion (FSP). This prospective randomised parallel study design included 160 infertile women < 38years of age where IUI was indicated. We recorded a detailed history and conducted a careful clinical examination with the performance of baseline investigations. Each patient was randomly allocated into two groups: Group sIUI (n = 80) and Group FSP (n = 80). The patients underwent two cycles of IUI for achieving clinical pregnancy. The conception of pregnancy among both groups was noted and compared. The mean age of the females, mean age of the male partners, and duration of marriage in Group sIUI and FSP were comparable (p > 0.05). Compared to the sIUI group, the FSP group had significantly higher patients who conceived (15.97% vs. 6.54%, P = 0.016). In the cases with unexplained infertility, in cycle 2, in the FSP group, there were significantly more patients who conceived (21.05% vs. 0.00%, P = 0.047). We conclude that FSP over two treatment cycles offers an advantage over the standard IUI and could replace the sIUI in specific indications such as unexplained infertility for artificial insemination. It could be used as an alternative for couples with non-tubal infertility before moving on to IVF treatment.