Acute aerobic exercise induces short-term neuroplasticity, although it remains unknown whether biological sex and ovarian hormones influence this response. The present study investigated the effects of biological sex and ovarian hormones on short-term neuroplasticity induced by acute aerobic exercise. Young active adults (n = 17 males and n = 17 females; 21 ± 2 years) participated in two sessions in which transcranial magnetic stimulation (TMS) measures were acquired immediately before and after a 20-min bout of moderate-intensity cycling at 65-70% of maximal heart rate. Females were tested in the follicular (~day 7) and luteal (~day 21) phases of the menstrual cycle. Males were tested on two sessions separated by ~14 days. Measures of motor-evoked potential (MEP) recruitment curves and short-interval intracortical inhibition (SICI) were obtained using TMS. Estradiol, progesterone, testosterone, brain-derived neurotrophic factor (BDNF), and insulin-like growth factor 1 (IGF-1) were measured in venous blood samples obtained prior to exercise. MEP recruitment curves increased and SICI decreased after exercise in both sexes, regardless of menstrual cycle phase. BDNF and IGF-1 were not different between sexes or across the menstrual cycle. Females had a greater estradiol to progesterone ratio (E:P) in the follicular phase compared to the luteal phase, while males had similar testosterone levels on both occasions. We conclude that biological sex and ovarian hormones do not impact short-term neuroplasticity induced by acute exercise. SIGNIFICANCE STATEMENT: Acute exercise induces short-term changes indicative of neuroplasticity within the primary motor cortex and corticospinal pathway. This research reveals that increases in corticospinal excitability and decreases in intracortical inhibition occur similarly in males and females, and that female hormones do not influence these changes. These findings may be used to assist with developing exercise interventions aimed at promoting neuroplasticity in both sexes.