Rainbow trout (Oncorhynchus mykiss) is one of the most widely cultivated freshwater fish species, with an annual global production of nearly 900,000 tonnes. However, a major challenge is its susceptibility to a wide range of pathogens, which leads to severe disease outbreaks and significant economic losses in fish farms. To mitigate these impacts, genetic improvement programs can be accelerated through quantitative trait loci (QTL) mapping aimed at identifying genomic regions that are associated with disease resistance. Nonetheless, variations among studies, as well as differences in the quality and density of genetic maps, often hinder the identification of consistent QTLs across traits and experiments. To overcome these limitations, meta-analysis has emerged as a powerful approach to enhance the reliability of QTL detection. In this study, a meta-QTL (MQTL) analysis was performed to identify stable genomic regions associated with pathogen resistance in rainbow trout. In total, 138 QTLs related to pathogen resistance traits were collected from previous studies, resulting in the identification of 26 MQTLs. The average confidence interval (CI) of these MQTLs was reduced to 2.5 times smaller than the original QTLs, demonstrating enhanced precision in their genomic positioning. Notably, the MQTL located on chromosome 3 exhibited the narrowest CI and the highest number of projected QTLs, whereas chromosome 8 contained the largest number of MQTLs. These regions might represent key genomic hotspots for pathogen resistance, providing valuable targets for functional genomics research and supporting the development of disease-resistant rainbow trout lines.