Background: Prenatal depression can negatively affect the physical and mental health of both mother and fetus. The aim of this study was to determine the effectiveness of yoga as an intervention in the management of prenatal depression. Methods: A systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted by searching PubMed, Embase, the Cochrane Library and PsycINFO from all retrieved articles describing such trials up to July 2014. Results: Six RCTs were identified in the systematic search. The sample consisted of 375 pregnant women, most of whom were between 20 and 40 years of age. The diagnoses of depression were determined by their scores on Structured Clinical Interview for DSM-IV and the Center for Epidemiological Studies Depression Scale. When compared with comparison groups (e.g., standard prenatal care, standard antenatal exercises, social support, etc.), the level of depression statistically significantly reduced in yoga groups (standardized mean difference [SMD], -0.59; 95% confidence interval [CI], -0.94 to -0.25; p = 0.0007). One subgroup analysis revealed that both the levels of depressive symptoms in prenatally depressed women (SMD, -0.46; CI, -0.90 to -0.03; p = 0.04) and non-depressed women (SMD, -0.87; CI, -1.22 to -0.52; p < 0.00001) were statistically significantly lower in yoga group than that in control group. There were two kinds of yoga: the physical-exercise-based yoga and integrated yoga, which, besides physical exercises, included pranayama, meditation or deep relaxation. Therefore, the other subgroup analysis was conducted to estimate effects of the two kinds of yoga on prenatal depression. The results showed that the level of depression was significantly decreased in the integrated yoga group (SMD, -0.79; CI, -1.07 to -0.51; p < 0.00001) but not significantly reduced in physical-exercise-based yoga group (SMD, -0.41; CI, -1.01 to -0.18; p = 0.17). Conclusions: Prenatal yoga intervention in pregnant women may be effective in partly reducing depressive symptoms.