Background Fibrocystic changes are a common benign condition in women aged 20–50. The medical intervention aims to stop fibrocystic disease progress and relieve the breast’s pain and tenderness. In the long-term, reversing the fibrocystic changes is also desirable. Methods In this randomized double-blind clinical trial, the effect of flaxseed oil on the severity of pain and breast nodularity was investigated against vitamin E. This study was conducted on 100 women with mastalgia. The intervention group received Flaxseed oil pearls and the control group received vitamin E pearl 200 IU twice a day for 2 months. The duration and severity of breast pain were evaluated by Cardiff chart and VAS (Visual Analogue Scale). The nodularity was assessed by Lucknow-Cardiff scale at baseline, then the first and second months of intervention. Results At baseline, there was no statistically significant difference between the two groups in characteristics. The breast pain improved in both groups during the first and second months of intervention (P-value within group< 0.001). However, the mean breast pain was not significantly different between the two groups at the end of the first and second month (P1= 0.54, P2= 0.73). Furthermore, the breast pain during four phases of the menstrual cycle showed no difference between vitamin E and flaxseed oil groups (menstruation phase= 0.76, follicular phase= 0.48, the first week of luteal phase= 0.86, the second week of luteal phase=0.30). The breast nodularity also decreased during the first and second months of intervention, yet no significant difference between the two groups was found (p= 0.9). Conclusions This study showed that flaxseed oil and vitamin E both could be effective in breast pain-relieving and decreasing nodularity with minimal side effects in contrast with the baseline. But there are no significant differences between these two agents. Larger scale prospective studies are needed to evaluate these effects in the long-term. Trial registration IRCT201612243014N18, Registration date: 2017-10-15.