Background: Laparoscopic appendectomy is a well-described surgical technique. However, concerns still exist regarding whether the closure of the appendiceal stump should be done with a clip, an endoloop, or other techniques. In this study, the effect of stump closure on duration of surgery and complications by endoclips was compared with endoloop in patients under laparoscopic appendectomy. The study was carried out as a prospective randomized clinical trial between 2013 and 2015 in Shariati Hospital of Tehran. Materials and Methods: Seventy-six patients under laparoscopic appendectomy were enrolled and randomly assigned to receive either endoclips or endoloop for stump closure. The results in terms of the operating time, length of hospital stay, and the complications were compared and analyzed between two groups. After collecting the essential data by using a checklist and examination of patients, the data were analyzed with SPSS.Results: The mean age was 23.13 ± 5.07 years and 44.7% of the patients were male. Moreover, in this study, it was seen that the mean duration of surgery was 23.2 min versus 21.5 min in endoloop and endoclips groups, respectively (P=0.021). There was no difference between hospital stay among two groups (P>0.05). Furthermore, the complications were same in two groups (P>0.05).Conclusion: The effect of stump closure with endoloop versus endoclips is not different for complications, but the duration of surgery was shorter in endoclips method. Both methods could be used based on the opinion of the surgeon without expecting a statistically significant difference in the results.