Background Venous thromboembolism is one of the critical complications of bariatric surgeries resulting in life-threatening outcomes. The benefits and duration of appropriate thromboprophylaxis in the morbidly obese patients stay unclear. The study aims to compare the benefits of in-hospital thromboprophylaxis versus extended thromboprophylaxis post-bariatric surgery among a cohort with a high prevalence of morbid obesity. Results A retrospective observational cohort study was conducted on 229 morbidly obese patients who had undergone bariatric surgery in a tertiary care teaching hospital in Saudi Arabia. Upon discharge, the patients were split either to receive no thromboprophylaxis or enoxaparin 40 mg once or twice daily for 14–21 days post-discharge. Primary outcomes were the clinical difference between the study groups in the percentage of patients who developed a symptomatic venous thromboembolic event during postoperative hospitalization or after discharge. Among patients who received no thromboprophylaxis (n = 119), no one developed a venous thromboembolic event, while, in the extended prophylaxis group (n = 110), 1.82% developed a non-fatal one (P = 0.23). Additionally, no significant difference in percentages of bleeding events occurred in both groups (p = 0.054). Conclusions The incidence of venous thromboembolism and bleeding events that occurred with extended thromboprophylaxis were deemed comparable and non-significant to the conventional in-hospital thromboprophylaxis. However, portal thrombosis stays an enigmatic complication despite its documented sparsity in literature.