Background Both exercise and pregnancy influence serum irisin concentration. Aim To determine how the interaction of pregnancy and exercise affects irisin level and whether various patterns of exercise adherence had different effect on irisin concentration. Methods It was a one-group pretest-posttest study among 9 Caucasian nulliparous healthy women in normal pregnancy (age 23 ± 3 years, 21 ± 2 weeks of gestation; mean ± SD) who participated in 8-week group fitness program. Before and after exercise intervention, we determined serum concentrations of irisin and selected parameters of lipid profile and glucose homeostasis markers. Results In active women, irisin slightly decreased with the development of pregnancy. After 8 weeks of exercising, irisin correlated negatively with fasting glucose (R = −0.922; p = 0.001), glycated hemoglobin (R = −0.784; p = 0.012), and insulin concentrations (R = −0.845; p = 0.004). In women exercising below recommended level, we observed a significant drop in irisin concentration, whereas in women exercising at least three times a week this myokine slightly increased (31% difference; 90% confidence limits ±28; a large, clear effect). Conclusions Irisin stimulated by prenatal exercise may improve glucose homeostasis markers in healthy women and compensate for metabolic changes induced by pregnancy. Moreover, the frequency of exercise may regulate the changes in exercise-induced irisin concentration.