In complete atrioventricular canal defect (CAVC), there are limited data on preoperative clinical and echocardiographic predictors of operative timing and postoperative outcomes. A retrospective, single-center analysis of all patients who underwent primary biventricular repair of CAVC between 2006 and 2015 was performed. Associated cardiac anomalies (tetralogy of Fallot, double outlet right ventricle) and arch operation were excluded. Echocardiographic findings on first postnatal echocardiogram were correlated with surgical timing and postoperative outcomes using bivariate descriptive statistics and multivariable logistic regression. 153 subjects (40% male, 84% Down syndrome) underwent primary CAVC repair at a median age of 3.3 (IQR 2.5–4.2) months. Median postoperative length of stay (LOS) was 7 (IQR 5–15) days. Eight patients (5%) died postoperatively and 24 (16%) required reoperation within 1 year. On multivariable analysis, small aortic isthmus (z score < − 2) was associated with early primary repair at < 3 months (OR 2.75, 95% CI 1.283–5.91) and need for early reoperation (OR 3.79, 95% CI 1.27–11.34). Preoperative ventricular dysfunction was associated with higher postoperative mortality (OR 7.71, 95% CI 1.76–33.69). Other factors associated with mortality and longer postoperative LOS were prematurity (OR 5.30, 95% CI 1.24–22.47 and OR 5.50, 95% CI 2.07–14.59, respectively) and lower weight at surgery (OR 0.17, 95% CI 0.04–0.75 and OR 0.55, 95% CI 0.35–0.85, respectively). Notably, preoperative atrioventricular valve regurgitation and Down syndrome were not associated with surgical timing, postoperative outcomes or reoperation, and there were no echocardiographic characteristics associated with late reoperation beyond 1 year after repair. Key preoperative echocardiographic parameters helped predict operative timing and postoperative outcomes in infants undergoing primary CAVC repair. Aortic isthmus z score < − 2 was associated with early surgical repair and need for reoperation, while preoperative ventricular dysfunction was associated with increased mortality. These echocardiographic findings may help risk-stratified patients undergoing CAVC repair and improve preoperative counseling and surgical planning.