Background: The benefit of primary anastomosis (PA) without a diverting stoma over Hartmann’s procedure (HP) for colorectal perforation remains controversial. We compared postoperative mortality and morbidity between HP and PA without a diverting stoma for colorectal perforation of various etiologies. Methods: Using the Japanese Diagnosis Procedure Combination database, we extracted data on patients who underwent emergency open laparotomy for colorectal perforation of various etiologies from July 1, 2010 to March 31, 2014. We compared 30-day mortality, postoperative complication rates, and postoperative critical care interventions between HP and PA groups using propensity score matching, inverse probability of treatment weighting, and instrumental variable analyses to adjust for measured and unmeasured confounding factors. Results: We identified 8500 eligible patients (5455 HP and 3045 PA). In the propensity score-matched model, a significant difference between the HP and PA groups was detected in 30-day mortality (7.7% vs. 9.6%; risk difference, 1.9%; 95% confidence interval [CI], 0.5–3.4). The inverse probability of treatment weighting showed similar results (8.8% vs. 10.7%; risk difference, 1.9%; 95% CI, 1.0–2.8). In the instrumental variable analysis, the point estimate suggested similar direction to that of the propensity score analyses (risk difference, 4.4%; 95% CI, −3.3 to 12.1). The PA group had significantly higher rates of secondary surgery for complications (4.6% vs. 8.4%; risk difference, 3.8%; 95% CI, 2.5–4.1) and slightly longer duration of postoperative critical care interventions. Conclusions: This study revealed a significant difference in 30-day mortality between HP and PA without a diverting stoma.