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Objectives: Only a few studies have suggested the association between ovarian cysts and serum estrogen levels during tamoxifen use. However, increased estrogen levels with ovarian cysts would affect the prognosis of breast cancer; this association has not yet been studied. We aimed to investigate the association between ovarian cysts and prognostic markers in premenopausal breast cancer patients undergoing tamoxifen treatment. Methods: A retrospective review of 65 premenopausal breast cancer patients who underwent tamoxifen treatment was performed. Serum hormone levels were measured either specifically between cycle days 2 and 5 in menstruating patients or at any time in amenorrheic participants. Results: The study population consisted of premenopausal patients with (n = 23) and without ovarian cysts (n = 42). Serum estradiol (E2) levels and tumor markers were not statistically different based on ovarian cyst status. In the subgroup analysis, serum E2 levels were significantly higher in menstruating women with ovarian cysts, and E2 levels were positively correlated with serum cancer antigen 15-3 and insulin-like growth factor-1 in these women. Conclusions: Ovarian cysts during tamoxifen use may affect the markers associated with the clinical course of premenopausal breast cancer.