The purpose of this study was to compare the effect of Phacoemulsification and Manual small incision cataract surgery (MSICS) on the corneal endothelium and to assess its impact on visual acuity and induced astigmatism. In this prospective randomized study, 100 cases were randomly selected with the help of lottery system. 50 cases underwent phacoemulsification (group 1) and 50 underwent MSICS (group 2) by a single surgeon. The endothelial cell count, central corneal thickness, best corrected visual acuity and induced astigmatism was measured preoperatively and postoperatively on day 1, 7, 28 and on day 42. Mean endothelial cell loss (cells/mm2) in group 1 at the end of six weeks was 538.64 (20.59%) and in group 2 was 485.66 (19.20%) which was statistically insignificant (p >0.05). The mean central corneal thickness was reduced in both the groups with a mean of 0.51±0.04 mm in group 1 and 0.50±0.03 mm in group 2 which was statistically insignificant. Postoperative best corrected visual acuity of more than 6/18 was found in 49 (98%) cases in each group at six weeks, and was statistically insignificant (p value > 0.05). Phacoemulsification group had statistically significant less mean postoperative astigmatism than MSICS group (p value < 0.05). Both groups gave similar statistically insignificant results in relation to endothelial cell loss, central corneal thickness and best corrected visual acuity at the end of six weeks, although the mean astigmatism was more in group 2 in comparison to group 1 with a statistically significant difference.