There are complex relationships between hormonal fluctuations associated with the menstrual cycle and various health and sports performance aspects. This study aimed to determine to what extent different menstrual cycle phases associated with a change in error scores in jumping and cutting movements, flexibility, and knee joint laxity values in female athletes. Participants were evaluated in the menstruation and ovulation phases of the menstrual cycle. Blood tests were performed from venous blood drawn at 8:00 am, after 12 hours of fasting. LH, FSH, estrogen, and progesterone hormone tests were conducted once during the menstruation phase and once during the ovulation phase. Landing Error Scoring System (LESS), Cutting Movement Assessment Score (CMAS), flexibility, and laxity were taken on the participants. The t-test and the Wilcoxon test were applied to analyze continuous variables. The McNemar test was used to examine categorical variables. The study was completed with 22 female athletes aged 20.45 ± 0.54 years. Participants comprised volleyball (n = 14, 63.6%) and handball (n = 8, 36.4%) athletes. Mean height 167.82 ± 1.52 cm, body weight 56.11 ± 1.43 kg, BMI 19.88 ± 0.33 kg/m2, menarche age 12,95 ± 1,21 menstruation duration 5,77 ± 0,75 (range: 4-7) days, menstrual cycle length was 29,32 ± 2,91 (range: 23-35) days, and the number of menstrual cycles in a year is 12,09 ± 0,25 (range: 10-15). As a result of the study, estradiol, LH, progesterone, and both knees' laxity values showed a statistically significant increase in the ovulation phase (p < 0.05). No statistically significant difference was observed between the phases in the flexibility test (p > 0.05). When the results of LESS and CMAS were examined, it was found that participants' total error scores and risk categories did not show a statistically significant difference between the phases (p > 0.05). LESS and CMAS analyses can be conducted and evaluated in both phases of the menstrual cycle, as it has been observed that the analyses yielded similar results in both phases.