In these GWAS, we discovered eight loci that are significantly associated with ME/CFS, including three near BTN2A2, OLFM4, and RABGAP1L genes that act in the response to viral or bacterial infection. Four of the eight loci (RABGAP1L, FBXL4, OLFM4, CA10) were associated at p < 0.05 with cases ascertained using post-exertional malaise and fatigue in the UK Biobank and the Netherlands biobank Lifelines. We found no evidence of sex-bias among discovered associations, and replicated in males two genetic signals (ARFGEF2, CA10) discovered in females. The ME/CFS association near CA10 colocalises with a known association to multisite chronic pain. We found no evidence that the eight ME/CFS genetic signals share common causal genetic variants with depression or anxiety. Our findings suggest that both immunological and neurological processes are involved in the genetic risk of ME/CFS.