Background: Considering the undesirable consequences of stress and anxiety in pregnancy and the role of midwives in providing emotional support for pregnant women, it is important to utilize non-medical therapies, such as spiritual counseling. Objectives: The present study aimed to determine the effect of spiritual counseling on stress and anxiety in pregnant women. Methods: This randomized controlled clinical trial recruited 112 pregnant women presenting to the health centers in Maragheh, Iran, in 2016 -17. The participants were assigned to two 56-member groups of control and intervention with a randomized block design. A socio-demographic questionnaire, the perceived stress scale, and the Spielberger state-trait anxiety inventory (STAI) were completed before and four weeks after the intervention through interviews with participants. Results: 55 participants in the counseling group and 56 in the control group were followed up and analyzed until the end of the study. The mean (± SD) scores of stress, state anxiety, and trait anxiety were 35.4 (± 4.5), 48.5 (± 4.8), and 47.4 (± 4.6) in the counseling group and 34.8 (± 3.6), 47.8 (± 4.1), and 49.0 (± 4.1) in the control group before the intervention, respectively. The mean (± SD) scores of stress, state anxiety, and trait anxiety were 34.8 (± 3.5), 48.0 (± 4.5), and 44.7 (± 4.0) in the counseling group and 37.8 (± 3.7), 49.7 (± 4.2), and 46.0 (± 3.8) in the control group four weeks after the intervention, respectively. According to ANCOVA for controlling the baseline scores after the intervention, the mean scores of perceived stress (adjusted mean difference = -3.4; 95% confidence interval = -2.3 to -4.4; P < 0.001) and state anxiety (-2.1; -3.6 to -5.5; P < 0.001) were significantly lower in the counseling group, while the two groups had no significant difference in terms of the mean scores of trait anxiety after the intervention. Conclusions: Spiritual counseling can control perceived stress and state anxiety of pregnant women. Therefore, spiritual counseling is recommended as a complementary and effective intervention in controlling the psychological problems of pregnant mothers.