Thrombosis is a common clinical feature associated with morbidity and mortality in coronavirus disease-2019 (COVID-19) patients. Cytokine storm in COVID-19 increases patients' systemic inflammation, which can cause multiple health consequences. In this work, we aimed to indicate the effect of Pfizer-BioNTech vaccination on the modulation of monocyte chemoattractant protein-3 (MCP-3), matrix metalloproteinase 1 (MMP-1), and tumor necrosis factor-alpha (TNF-α) levels, and other systemic inflammatory biomarkers that associates with COVID-19 severity in patients who suffers from thrombosis consequences. For this purpose, ninety people were collected from Ibn Al-Nafees Hospital and divided into three groups each of which contained 30 people, 15 of them were venous thromboembolism (VTE) positive and the other were VTE negative. The three groups were non-vaccinated COVID-19, vaccinated COVID-19, and control. The levels of MCP-3 and TNF-α were significantly (p < 0.05) increased in vaccinated and non-vaccinated COVID-19 patients regardless of their thrombosis condition, while MMP-1 level was non-significantly (p > 0.05) higher in vaccinated patients compared to control. MCP-3 and TNF-α were correlated positively with D-dimer (r = 0.544 and r = 0.513, respectively) in non-vaccinated patients, while MMP-1 and TNF-α were correlated positively with D-dimer (r = 0.624 and r = 0.575, respectively) in vaccinated patients. The odds ratio of MCP-3 (2.252), MMP-1 (1.062), and TNF-α (1.360) were reduced in vaccinated patients (2.093, 1.022, and 1.301 for MCP-3, MMP-1, and TNF-α respectively). Thus, MCP-3 plays a vital role in COVID-19 pathophysiology, and vaccination can reduce the risk of developing VTE in COVID-19 patients, and improve the inflammatory condition of patients. © 2024 Elsevier B.V.