OBJECTIVES: This study aims to compare the clinical performance of 3D printed endocrowns (ECs) and prefabricated zirconia crowns (PZRCs) in restoring pulpotomized primary molars, over 3, 6, and 12 months. METHODS: Thirty pulpotomized mandibular primary molars in 16 children aged 4-8 years were randomized with a 1:1 allocation ratio into two groups: group (A), PZRCs, and group (B), 3D-printed ECs. All restorations were evaluated for esthetic, functional, and biological properties using FDI criteria at 3-, 6-, and 12-month intervals. Restorations requiring repair or replacement (a total restoration score of 4 or 5, respectively) were recorded as failures. For each outcome variable, the Mann-Whitney U test was used for intergroup comparisons, while Friedman's test was used for intragroup comparisons, followed by the Nemenyi post hoc test. The significance level was set at p ≤ 0.05. RESULTS: No statistically significant difference in survival times between PZRCs and ECs was found (12 and 11.36 months, respectively). Both restoration types showed a clinical success rate of 64.3 %. No statistically significant difference was found between the esthetic success of PZRCs and ECs (92.9 % and 71.4 %, respectively), matching their functional success rates. Similarly, no statistically significant difference was observed in the biological success of ECs and PZRCs (78.6 % and 64.3 %, respectively). CONCLUSION: 3D-printed ECs can be a promising and convenient alternative to full-coverage restorations in pulpotomized primary molars for up to one year. CLINICAL SIGNIFICANCE: Restoration of pulpotomized primary molars using 3D-printed ECs offers a more conservative and esthetic option with minimal trauma to gingival tissues and reduced chair time, which is crucial for pediatric patients. CLINICAL REGISTRATION NUMBER: NCT04909827.