Patients with COVID-19 exhibit distinct laboratory findings that are compatible with a pro-thrombotic state, in which the key associated underlying episode to thrombotic complications is an excessive inflammatory response of the host to infection. The aim of the present study was to evaluate routine prophylaxis for pulmonary thromboembolism (PTE) at a teaching school and the effect of COVID-19 on the prevalence of deep vein thrombosis (DVT) and PTE in the year 2020. The study was conducted analyzing records the patients, monthly prevalence of adequate prophylaxis and the monthly incidence of DVT and PTE in patients with moderate to high risk based on the Wells score in the year 2020, with an investigation of the effect of COVID-19 on this incidence at São José do Rio Preto Hospital. An analysis was performed of hospital data on the prevalence of adequate prophylaxis for deep vein thrombosis and pulmonary embolism in patients with moderate to high risk for PTE based on the Wells score in the year 2020. For prophylaxis, conventional and low molecular weight heparin, rivaroxaban, warfarin, antithrombotic elastic stockings and pneumatic boots were used, depending on the needs of each patient. Our results show that June and July were the peaks of the COVID-19 pandemic, with a significant increase in the incidence, going from an annual level of 0.29% to 0.88%. The monthly mean incidence went from 0.13% through June to 0.46% from July to December; this difference was statistically significant (p = 0.002, Mann-Whitney U test). The coronavirus has increased the incidence of deep vein thrombosis and pulmonary embolism, suggesting a failure in mechanisms of prophylaxis for PTE implanted prior to COVID-19.