This study aimed to conduct a systematic meta-analysis to compare the seroprevalence of major abortion-causing parasites, particularly Neospora caninum, between industrial and semi-industrial dairy farms in two major Iranian provinces, Isfahan and Chaharmahal va Bakhtiari. A comprehensive search and integration of existing epidemiological, serological, and molecular studies from the region were performed. Data were pooled and statistically analyzed using random-effects models, specifically the DerSimonian-Laird method, to account for heterogeneity across studies. The meta-analysis revealed a significantly higher overall seroprevalence of N. caninum in Isfahan Province. The seroprevalence in dairy cattle with a history of abortion in Isfahan was 32.1%, peaking at 74.6% in herds with confirmed contact with wild canids. In contrast, the prevalence in aborted fetuses in Chaharmahal va Bakhtiari was notably lower at 11%. The statistical comparison showed a significant difference (p < 0.05) between the two provinces, with high heterogeneity (I² = 87.26%) indicating substantial regional variation. The national pooled prevalence in aborted fetuses was estimated at 34.8%. These findings unequivocally identify N. caninum as a primary parasitic agent of bovine abortion in the studied regions, with the risk being substantially higher in industrial farms in Isfahan. The study concludes that targeted preventive strategies, including strict management of definitive host access and vaccination programs, are urgently needed, especially in high-prevalence areas like Isfahan, to mitigate significant economic losses and improve reproductive herd health.