Background Trypanosomosis is a haemoprotozoan disease, mostly transmitted by the tsetse fly (Glossina spp.), it causes severe disease in humans and animals in Sub-Saharan Africa (SSA). The disease results in loss of livestock and agricultural productivity with severe socio-economic impacts. In Ethiopia, bovine trypanosomosis is widely distributed in western and south-western parts of the country. It is estimated that some 10 to 14 million heads of cattle in Ethiopia are exposed to the risk of trypanosomosis. Methods This study describes the prevalence of bovine trypanosomosis in Ethiopia through a meta-analysis. A comprehensive search was conducted on PubMed and non-PubMed indexed articles were also incorporated based on expert suggestion. Eligible studies were selected by using inclusion and exclusion criteria. Pooled prevalence was estimated by random effect model. Publication bias and the variation in prevalence estimates attributed to heterogeneity were also assessed. Results Twenty-four studies with relevant prevalence data were identified and included in the analysis. The apparent prevalence of bovine trypanosomosis varied from 1.38 to 17.15 %. The pooled estimate of bovine trypanosomosis prevalence across studies for the entire period was 8.12 % (95 % CI: 6.88; 9.35), ranging from 10.27 % (95 % CI: 7.34; 13.20) in the late 1990s and early 2000s, to 6.81 % (95 % CI: 5.00; 8.62) after 2010. Sub-analysis by region revealed wide variations in prevalence. The highest estimated regional prevalence was 13.30 % (95 % CI: 7.73; 18.88) in Benishangul Gumuz Regional state. A high degree of heterogeneity was observed in most pooled estimates and even after sub-group analysis. The visual inspection of the funnel plot and the Egger’s regression asymmetry coefficient [b = 2.18] (95 % CI = −1.09, 5.46; p > 0.05) did not suggest the presence of publication bias. T. congolense and T. vivax were reported to be the predominant causative agents. From the total positive animals, 45.5 and 44.3 % of the infections are accounted to T. congolense and T. vivax, respectively. Conclusions The meta-analysis showed a significant reduction in prevalence of bovine trypanosomosis in recent years, but the reduction is not to the lowest necessary level. Since T. vivax is reported to be one of the most important trypanosome species involved, efforts should also be made to control the mechanical transmission by biting flies. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1404-x) contains supplementary material, which is available to authorized users.