Background: In recent years high intensity interval training (HIIT) has grown in popularity, however it rarely represent training interventions in experimental studies in pregnant populations so far. Therefore, in this study we aimed at assessing the changes in depressive symptoms, fear of childbirth, fear of Covid-19, quality of life after an 8-week supervised online HIIT program, compared to an educational (self-performed physical activity) program. Methods: We conducted a randomized control trial among 54 Caucasian women in uncomplicated, singleton pregnancy (age 32 ± 4 years, 22 ± 4 week of gestation; mean ± SD). There were 34 women in the experimental group, who participated in an 8-week high intensity interval training program (HIIT group). The comparative group was constituted of 20 pregnant women who attended 8-week educational program (EDU group). Results: The most important finding was that after intervention the mental health improved somewhat in both groups, but only in the HIIT group the improvement was statistically significant. The positive trends in lowering the severity of depressive symptoms, fear of childbirth, and fear of Covid-19 were observed in both groups, however the positive response to the intervention was stronger in the EDU group. As secondary outcome, there was a significant decrease in cardiorespiratory fitness level in the EDU group, while the HIIT group maintained unchanged level of maximal oxygen uptake. Conclusions: HIIT can be recommended for women with uncomplicated pregnancies to prevent depression and anxiety symptoms. However, more research is needed to determine the effectiveness of prenatal HIIT in pregnant women in various psychological conditions.Trial registration: We conducted this study in Poland, in 2021. It was approved by the Bioethics Commission at the District Medical Chamber in Gdansk (KB - 8/21). The full study protocol was registered in ClinicalTrials.gov (NCT05009433).