To determine the effect of an education program and/or pill count on the change in hemoglobin levels and the prevalence of anemia in pregnant women. A randomized, factorial design controlled trial was conducted at the Tribhuvan University Teaching Hospital, Nepal. A total of 320 eligible pregnant women receiving prenatal care were randomized into four groups (control, education, pill count and education with pill count) by block randomization with allocation concealment. All recruited women received conventional routine prenatal care with a daily dose of 60 mg iron supplementation. In addition, the education group received an education program. Pill counting was done for the pill count group at their routine prenatal visits. The education with pill count group received both the education program plus pill counting. Baseline hemoglobin at the recruitment phase and follow-up hemoglobin after three months of recruitment were measured. Changes in hemoglobin levels and anemia prevalence were analyzed and compared between groups. The education only and education with pill count groups had significantly higher hemoglobin changes (0.23 and 0.26 g/dL, respectively) than the control group (P < 0.01). Anemia was reduced by 59% in the education group and by 65% in the education with pill count group, compared to the control group (P < 0.05). Pill count alone significantly improved neither the hemoglobin level nor anemia prevalence compared to the control group. An education program along with routine iron supplementation can improve hemoglobin levels and reduce anemia prevalence in pregnant women. Pill count as a measure of compliance has no additional effect on improving hemoglobin status.