Background Venous thromboembolism (VTE) is a serious complication in hospitalized patients. It is associated with considerable morbidity and mortality. Therefore, its prevention is of great importance. There is paucity of data on the incidence of VTE in hospitalized patients in Cameroon. The aim of this study was to determine the incidence of symptomatic VTE, its risk factors and the proportion of patients at risk that receive thromboprophylaxis in patients hospitalized in the medical and surgical units in two hospitals in the South West Region of Cameroon. Methods A prospective study was performed in the medical and surgical units from January to March 2018. All consecutive eligible patients admitted for at least 3 days were included. Patient profile and risk factors were recorded. Patients were followed and evaluated for signs and symptoms of VTE until discharge from hospital. Suspected VTE was confirmed using compression ultrasonography and computed tomography. Results A total of 314 patients were included of which 58.7% were females. The mean age was 46±17.9 years. Patients aged <40 years represented 42% of the study population. Three cases of symptomatic VTE were recorded. The incidence of symptomatic VTE was 1% (95% CI: 0.3–2.8%). The prevalence of VTE risk was 93.6% with 32.5% being at high risk. The risk was 94.6% in medical patients and 92.8% in surgical patients. Among the patients at risk, only 32.5% received thromboprophylaxis. Thromboprophylaxis was significantly higher in surgical patients compared to medical patients (45.2% versus 18.7%; p<0.0001). Conclusion The incidence of VTE in hospitalized medical and surgical patients appeared low but likely underestimated considering the high prevalence of patients at risk of VTE coupled with the underutilization of thromboprophylaxis. Clinicians should assess risk of VTE in conjunction with the clinical situation to determine the most appropriate type of prophylaxis as well as the duration of prophylaxis for VTE.