Introduction Venous thrombosis is a well-known complication of cancer disease, especially in Urology. However, even though proper antithrombotic prophylaxis is crucial in most urological procedures, we have insufficient high-quality studies on this topic. The European Association of Urology (EAU) Guidelines are outdated and lack data on COVID-19 increased risk of thrombosis. This review aimed to summarize data on thromboprophylaxis after radical prostatectomy, cystectomy, and nephrectomy during COVID-19 pandemic. Material and methods A thorough analysis of the EAU Guidelines of Thromboprophylaxis was performed and compared to PubMed search, considering updated literature on thromboprophylaxis of radical prostatectomy, cystectomy, nephrectomy, as well as COVID-19 influence on venous thrombosis and urological practice. Results Each patient should be evaluated individually to balance bleeding and venous thromboembolism (VTE) risk. There is still much uncertainty in low and medium-risk patients and all endoscopic procedures, where thromboprophylaxis could be omitted. Patients with COVID infection bear a significantly higher risk of VTE. All patients should be tested for COVID infection prior to a planned surgery during bursts of infections, undependably of vaccination status. Efforts to maintain early cancer diagnosis and treatment during the pandemic should be maintained. Conclusions The quality of evidence is inadequate, and when deciding on thromboprophylaxis, we need to base it on individual risk, cancer advancement, procedure type, and our own experience.