Background: Pain is a highly prevalent side effect of breast cancer therapy. High pain levels can reduce treatment adherence and increase discontinuation rates for hormonal therapies (HT) while reducing quality of life. We conducted a multi-site, blinded phase II RCT examining the efficacy of ω3 fatty acid (fish oil) supplementation versus ω6 fatty acid (soybean oil) supplementation for improving pain through the URCC NCORP. Methods: Breast cancer survivors between 4-36 months post-adjuvant therapy were randomized into 3 arms: 1) High-dose ω3 (ω3; 6 g/day), 2) Low-dose ω3/ω6 (ω3/ω6; ω3: 3 g/day and ω6: 3 g/day) and 3) High-dose ω6 (ω6; 6 g/day) for 6 weeks. Pain was assessed via the Brief Pain Inventory (BPI) at pre- and post-intervention. Serial blood was collected for serum fatty acid and inflammatory biomarker analysis. ANCOVAs, controlling for baseline pain and type of HT (AI, tamoxifen, or none), were used to calculate mean change from baseline to post-intervention for this secondary data analysis. Results: 108 female breast cancer survivors were accrued (93% white, mean age = 60). Biochemical blood analyses confirmed high compliance in all arms with minimal contamination. Mean baseline Worst Pain levels did not differ between groups (ω3 = 4.9, ω3/ω6 = 5.6, ω6 = 4.7; p = 0.43). The mean Worst Pain score decreased by 0.8 points for ω3, by 0.8 points for ω3/ω6, and by 1.7 points for ω6 (ω3 vs ω6 p-value = 0.18). The mean change in Current Pain score was more pronounced (Change score: ω6 = −1.8 vs ω3/ω6 = −0.8 vs ω3 = −0.5; ω3 vs ω6 p = 0.05) and indicated a dose-response. Similar changes were found for Average Pain and Least Pain but the differences were not significant. The ω6 group had a significant reduction in the inflammatory biomarker IL-6 compared to the ω3 group (IL-6 change: ω3 = +0.17 vs ω6 = −0.30; p < 0.01). Conclusions:ω6 supplementation reduced pain levels compared to ω3 supplementation in breast cancer survivors. ω6 also significantly reduced IL-6 levels compared to ω3, indicating a potential mechanism of action. Further research is needed on the effects of ω6 fatty acids in cancer patient. Funding: NCI R03CA175599 & UG1CA189961. Nordic Naturals Inc. supplied all study agents. Clinical trial information: NCT02352779