Introduction It is still unclear whether Crohn's disease (CD) might be associated with diminished ovarian reserve (OvR) and factors influencing anti‐Mullerian hormone (AMH) levels in CD are poorly known. Material and Methods We conducted a comprehensive literature search of multiple electronic databases from inception to June 2022 to identify all studies reporting AMH levels or factors associated with diminished OvR in patients with CD. Results Of the 48 studies identified in our search, eight (including 418 patients with CD) were finally included. The mean difference (95% confidence interval [CI]) in the AMH level between pooled CD patients and controls was −0.56 (−1.14 to 0.03) ( p = 0.06). A history of CD‐related surgery was not associated with a lower OvR (odds ratio, OR [95% CI] 1.34, [0.66–2.7]; p = 0.4). While disease activity and perianal disease seems associated with a low OvR, disease location (L2 vs. L1, OR [95% CI] = 95% CI [0.47–7.4]; p = 0.4) and L3 vs. L1 (OR [95% CI] = 1.44 [0.67–3.12]; p = 0.3), CD medication, and disease behavior were not. Conclusions Our systematic review and meta‐analysis did not identify a significantly low OvR in patients with CD. Contrary to CD‐related surgery risk factor, active disease was associated lower AMH levels.