The purpose of this study is to evaluate post-operative length of stay (LOS) following surgical repair of congenital heart defects (CHD) and to investigate baseline pre-operative factors and predictors of post-operative LOS (pLOS). Retrospective chart review of all cases of corrective surgery for CHD performed at the Pediatric Cardiology Unit, King Abdulaziz University Hospital, Jeddah during January 2013—December 2016. Baseline demographics, clinical factors, pre-operative, intra-operative, post-operative cardiac and extra-cardiac complications were analyzed as independent factors of pLOS using stepwise linear regression. Kaplan–Meier (KM) survival analysis was used to analyze the correlation of pLOS (in days) with the independent variables and estimate the probability to exceeding a given pLOS. A total 191 patients (52.4% male, 49.7% aged ≤ 1 year) were included with a median [range] LOS = 10 [3, 158] days. Several baseline clinical factors were associated with longer pLOS such as complex CHD types (tetralogy of Fallot, transposition of great arteries, etc.), high-risk RACHS categories and low weight at surgery. Independent risk factors of pLOS included pre-operative hemoglobin level (unstandardized regression coefficient: B = 2.96, p = 0.036) as the only pre-operative predictor of LOS, besides intra-operative complications (B = 11.72, p = 0.009) and posto-perative factors including MV duration (B = 9.39, p < 0.001), diet/feeding problems (B = 10.27, p = 0.001) and drain tube stay (B = 3.82, p = 0.003). KM survival curves confirmed that these factors increased the probability for longer LOS. Post-operative LOS was associated with several baseline and peri-operative factors; however, it was independently predicted by abnormal baseline hemoglobin level, the occurrence of intra-operative complications, besides post-operative feeding problems, chest drain stay, and MV duration.