Objective To investigate potential associations between dietary intake of polyunsaturated fatty acids (PUFA) and pain patterns in early rheumatoid arthritis (RA) patients after three months of methotrexate (MTX) treatment. Methods We included 591 early RA patients with MTX monotherapy from a population based prospective case-control study, the Epidemiological Investigation of Rheumatoid Arthritis (EIRA). Dietary data on PUFA (food frequency questionnaires) were linked with data on unacceptable pain (visual analogue scale (VAS) >40mm), non-inflammatory/refractory pain (VAS >40mm and C-reactive protein (CRP) <10mg/L) and inflammatory pain (VAS >40mm and CRP >10mg/L) after three months. Statistical analysis included logistic regression. Results After three months of MTX treatment, 125 patients (21.2%) had unacceptable pain, of which 92 patients had refractory pain and 33 patients had inflammatory pain. Omega-3 fatty acid (FA) intake was inversely associated with unacceptable pain and refractory pain (OR=0.57 [95% CI 0.35-0.95] and OR=0.47 [95% CI 0.26-0.84], respectively). Omega-6 to -3 FA ratio, but not omega-6 FA alone, was directly associated with unacceptable pain and refractory pain (OR=1.70 [95% CI 1.03-2.82] and OR=2.33 [95% CI 1.28-4.24], respectively). Furthermore, PUFA was not associated with neither inflammatory pain nor CRP and erythrocyte sedimentation rate at follow-up. Omega-3 FA supplementation was not associated with any pain patterns. Conclusion Omega-3 FA was inversely associated with, and omega-6 to -3 FA ratio was directly associated with unacceptable and refractory pain, but not with inflammatory pain or systemic inflammation. The inverse association between omega-3 FA and refractory pain may have a role in pain suppression in RA.