Animal trypanosomosis is a significant livestock disease with economic and social repercussions, reducing the supply of animal products and restricting the utilization of animals for traction and transportation. In Ethiopia, it is prevalent and poses a major hindrance to the advancement of animal production. This repeated cross-sectional study was aimed at assessing seasonal variation in bovine trypanosomosis prevalence and tsetse fly density and identifying the potential risk factors in the Loka Abaya and Derara districts of the Sidama National Regional State. Blood samples were collected from 964 cattle, 484 samples during the dry season, and 480 during the wet season. The buffy coat method was employed to analyze these samples. Furthermore, 78 standard NGU traps were set up at various locations in the two districts during both seasons for entomological investigation. The overall apparent prevalence of trypanosomosis was 9% (95% CI 7.3-11.0), without a significant difference (p > 0.05) between the dry season (7.4%) and wet season (10.6%). The apparent prevalence was significantly higher in Loka Abaya (11.8%) than in Derara (6.3%) district (OR = 2.04; p = 0.003) and in cattle with black coat color (29%) than in mixed color (6.8%) (OR = 5.3; p < 0.001). The majority of infections were caused by Trypanosoma congolense (70%), followed by T. vivax (29%), and mixed infections (1%) with the two species. The average packed cell volume (PCV) was significantly (p < 0.0001) lower in infected animals (20.7 ± 4%) compared to uninfected ones (25.5 ± 5.4%), in cattle examined during the dry season (24.1 ± 6%) versus the wet season (26.1 ± 4.7%), in cattle sampled from the Loka Abaya district (24.2 ± 5.5%) versus Derara district (26 ± 5.3%), and in cattle with poor body condition (23.6 ± 5.7%) compared to those with good body condition (26.5 ± 5.3%). A total of 5282 flies were captured during the study, with 4437 (84%) being tsetse flies (Glossina pallidipes), 439 (8.3%) Tabanids, 190 (3.6%) Stomoxys spp., and 216 (4.1%) Musca spp. The apparent density (AD) of G. pallidipes was 28.4 flies/trap/day, showing no statistically significant difference between wet (32.1) and dry (24.6) seasons (p > 0.05). The AD of G. pallidipes was significantly (p < 0.001) higher in the Loka Abaya district (57.3) than in the Derara district (0.9). The study highlights a moderate trypanosomosis apparent prevalence and high AD of G. pallidipes, showing significant variation between the study districts but no seasonal difference. The observed apparent prevalence of trypanosomosis and tsetse fly density notably affects animal health and productivity. As a result, strategies for vector control like insecticide-treated targets, trypanocidal medications for infected animals, and community-based initiatives such as education and participation in control programs are recommended.