Introduction: Heparin-induced thrombocytopenia (HIT) is a life-threatening disease associated with thromboembolic complications. Therefore, its treatment should comprise non-heparin anticoagulants. As opposed to direct thrombin inhibitors (DTI) and danaparoid, fondaparinux use is generally regarded as off-label. Purpose: To perform a meta-analysis to appraise fondaparinux efficacy and safety in the setting of HIT. Methods: We systematically searched Embase, MEDLINE, Web of Science, Cochrane CENTRAL and Google Scholar databases, using the terms “heparin-induced thrombocytopenia” and “fondaparinux”, form inception to June 1, 2020. Studies targeting thrombotic complications, bleeding events, platelet count and mortality were included. The primary endpoint was a composite of arterial and venous thromboembolism, amputation, gangrene and HIT-related mortality. Therapeutic arms were those of fondaparinux and a standard non-heparin anticoagulant. A random-effects model with Mantel-Haenszel method was performed to calculate pooled odds ratios (OR) and their 95% confidence interval (CI). Results: We encompassed 7 retrospective studies, which accounted for 630 patients, of which 302 were under fondaparinux. The remaining were treated with danaparoid, argatroban, lepirudin or bivalirudin. There were 109 primary endpoint events, 80 hemorrhages, 13 persistent or recurring thrombocytopenia cases and 98 deaths. Fondaparinux was found not only to numerically reduce thromboembolism (6 studies, OR 0.28, 95% CI 0.06-1.20, P 0.09, i 2 45%) but also to significantly lessen primary endpoint events (7 studies, OR 0.26, 95% CI 0.10-0.67, P 0.006, i 2 66%). In parallel, a tendency towards a lower rate of bleeding with fondaparinux use was also unveiled (7 studies, OR 0.78, 95% CI 0.50-1.21, P 0.27, i 2 0%). Likewise, thrombocytopenia cases were less common in the fondaparinux arm (4 studies, OR 0.16, 95% IC 0.05-0.57, P 0.004, i 2 0%). Finally, fondaparinux use was also associated with a survival benefit (6 studies, OR 0.26, 95% IC 0.08-0.90, P 0.03, i 2 54%). Conclusions: Fondaparinux seems to be at least as safe and more effective than other non-heparin anticoagulants, in the setting of HIT. Prospective studies are needed to demonstrate this hypothesis.