The observed higher rate of appendectomy despite the success of the conservative (non-surgical) approach might be due to the lack of awareness. The cecal appendix is not merely rudimentary because of its role on the gut microbiota and the host immune system. This meta-analysis aimed to assess the association of appendectomy at baseline with inflammatory bowel diseases. The PubMed, Cochrane library, and Google Scholar databases were systematically searched for relevant articles. The keywords used were inflammatory bowel disease, appendicitis, appendectomy, gut lymphoid tissue, Crohn's disease, ulcerative colitis with protean "AND" or "OR". No limitation was applied to the time of publication. Out of the 622 references found, 32 full texts were screened, and only eight studies fulfilled the inclusion and exclusion criteria. There were fifteen cohorts from eight studies (five were published in Europe, two were from Asia, and one from South America with 9703 participants and 1150 events). The overall effects showed a negative impact of appendectomy on the rate of Crohn's disease, odd ratio, 0.311, 95% CI, 1.20-8.05, P-value = 0.02. In ulcerative colitis and appendectomy arm, appendectomy was protective for ulcerative colitis, odd ratio, 0.44, 95% CI, 0.35-0.55, P-value = 0.001. Significant heterogeneities were observed (95% for Crohn's disease prevalence, P-value <0.001, and Chi-square, 118.69, and 86% for ulcerative colitis arm P-value <0.001, and Chi-square, 51.54). Appendectomy was protective against ulcerative colitis, however, the impact was negative on Crohn's disease. Further studies assessing the effects of appendectomy on the prognosis of ulcerative colitis are recommended.