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Fatigue is a common and impactful complaint among pregnant women, particularly prevalent during the first and third trimesters, and can adversely affect maternal and fetal physical and psychological health. Limited interventional evidence, especially regarding non-pharmacological approaches, highlights the need for safe and effective strategies. This study aimed to determine the effect of regular exercise on fatigue in pregnant women. This randomized controlled trial included 68 pregnant women between 20 and 28 weeks of gestation, without any contraindications for exercise, were randomly assigned to intervention and control groups using block randomization. Exclusion criteria included unwillingness to continue participation or absence from more than two sessions. The intervention group participated in weekly childbirth preparation classes, which included 30 min of exercise, and were instructed to perform home-based exercises at least four times per week for 45 min each session. The control group performed only the exercises taught during the weekly classes. Fatigue was measured using the Multidimensional Fatigue Inventory (MFI-20) before and after the 8-week intervention, and data were analyzed using ANCOVA after adjusting for baseline scores. After adjustment for baseline fatigue scores, BMI, gestational week, and parity, the intervention group showed significantly greater reductions in general (MD = 1.73; 95% CI: -3.30 to − 1.17; p < 0.05) and mental fatigue (MD = MD = -1.04; 95% CI: -2.01 to -0.07; p < 0.05), as well as improved motivation (MD = -3.77; 95% CI: -5.10 to -2.44; p < 0.001) compared with the control group (p < 0.05). No significant differences were found for other fatigue subscales and mental fatigue (p > 0.05). Regular low-to-moderate intensity exercise significantly reduced general and mental fatigue and was associated with improved motivation in pregnant women. No significant change was observed in total fatigue or other subscales. Also, no adverse events were observed among participants. It is recommended that such feasible and safe interventions be integrated into routine prenatal care programs. This randomized controlled trial was registered in the IRCT system (IRCT20180218038783N9; registration date: April 19, 2024).