Pregnant women may experience pain and discomfort during pregnancy, especially in areas such as the lower back and pelvic girdle. Pain in pregnancy is associated with poor quality of life, and because it is a common occurrence, pregnant women may be offered several resources to prevent discomforts throughout pregnancy, such as engaging in physical activity. This study was a meta-analysis of randomised controlled trials (prospectively registered in Prospero, registration number: CRD42023451320) aimed to assess the effects of physical activity during pregnancy on maternal pain and discomfort. We analysed 16 randomised clinical trials. The results of these analyses indicate that women who performed physical activity had significantly less intensity of pain (z = <2.69, p = <0.007; SMD = −0.66, 95% CI = −1.13, −0.18, I2 = <91%, Pheterogeneity = <0.001) and a reduction observed in the disability questionnaire (z = <2.37, p = <0.02; SMD = −0.80, 95% CI = −1.47, −0.14, I2 = <91%, Pheterogeneity = <0.001), and overall reduced general pain (z = <3.87, p = <0.001; SMD = −0.56, 95% CI = −0.84, −0.27, I2 = <86%, Pheterogeneity = <0.001) than women who did not practice physical activity during pregnancy. In conclusion, physical activity during pregnancy could effectively help to diminish pain intensity, reduce disability due to pain, and generally reduce pain.