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Abstract Background Blastocystis is a common intestinal protozoa found in animal and human fecal samples, with over 1 billion individuals infected worldwide. Since domestication, dogs and cats have had a close bond with humans. However, their close proximity poses a potential health risk since they may harbor several zoonotic agents. A global estimate of Blastocystis infection and subtype (ST) distribution in dogs and cats would therefore be of great health importance to humans. Methods We performed a comprehensive systematic search of four English-language databases (PubMed, Scopus, Google Scholar, Web of Science) for relevant articles up to 8 November 2021. The random-effects model was used to make pooled estimates with confidence intervals (CIs). Results In total, we identified 49 publications that met our inclusion criteria and subsequently analyzed the 65 datasets in these articles, of which 23 and 42 datasets were on cats and dogs, respectively. Among the 2934 cats included in the 23 datasets, which involved 16 countries, the prevalence rate of Blastocystis infection was 9.3% (95% CI 5.3–15.9%). The prevalence of Blastocystis infection was slightly lower [7%, 95% CI 4.7–10.4%) among the 7946 dogs included in the 42 datasets, involving 23 countries. The sensitivity analysis showed that no remarkable variation in the estimates upon the stepwise removal of each dataset. Higher ST diversity was found among the examined dogs (ST1-8, ST10, ST23, ST24) than among cats (ST1-4, ST10, ST14). Among dogs, ST3 was the most frequent ST (41.3%), followed by ST2 (39.3%), ST1 (30.9%), ST4 (13.4%), ST8 (12.7%), ST10 (11%) and ST5 (8.1%). Also among dogs, each of ST6, ST7, ST23 and ST24 was observed in only one study. Of the ST found in the cats examined, ST4 (29.5%), followed by ST10 (22.5%), ST1 (19.8%) and ST3 (17.6%) were the most common. A single study also reported the presence of both ST2 and ST14 in cats. With respect to zoonotic Blastocystis STs (ST1–ST9 and ST12), eight were reported from dogs (ST1-ST8) and four were isolated from cats (ST1–ST4), showing the implication of dog and cats in zoonotic transmission. Conclusions Taken together, our results show that elucidation of the true epidemiology and ST distribution of Blastocystis in dogs and cats demands more comprehensive studies, particularly in the negelected regions of the world. Graphical Abstract |