Objectives: It is unclear whether exercise modality (moderate-intensity continuous [MCE]; high-intensity interval [HIE]) and menstrual cycle phase (follicular [FP]; luteal [LP]), individually or in combination, mediate the commonly observed exercise-induced elevation in cardiac troponin T (cTnT). This study examines cTnT responses to MCE and HIE during both the FP and LP. Design: Randomised crossover study. Methods: Seventeen healthy, eumenorrheic women completed four trials including MCE (60% VO steady-state cycling until 300 kJ) and work‐equivalent HIE (repeated 4-min cycling at 90% VO interspersed with 3-min rest) during both the FP and LP. The FP and LP were verified based on ovarian hormones. Serum cTnT was assessed using a high-sensitivity assay before, immediately after, and 1 (1HR), 3 (3HR) and 4 (4HR) hours after exercise. cTnT values were corrected for plasma volume changes. Results: cTnT was significantly elevated (p < 0.05) post-exercise in both MCE (at 3HR and 4HR) and HIE (at 1HR, 3HR and 4HR). No statistically significant difference (p > 0.05) in peak post-exercise cTnT, which mostly occurred at 3HR, was seen among the four trials (median [range], ng l: 5.2 [1.7–18.1] after MCE during FP; 4.8 [1.7–24.9] after MCE during LP, 8.2 [3.9–24.8] after HIE during FP and 6.9 [1.7–23.1] after HIE during LP). Conclusions: A single 300 kJ bout of both MCE or HIE resulted in a significant post-exercise increase in cTnT, with no differences in peak cTnT response between menstrual cycle phases or between exercise modes, but the cTnT elevation occurs slightly earlier after HIE.