Background Iron folate supplementation is a cost-effective way of reducing iron deficiency anemia, low birth weight, and neural tube defects in resource-limited countries like Ethiopia. Late to start and poor adherence to iron-folate supplement has restricted its effectiveness. The aim of this study was to determine the time to start and adherence level of iron-folate supplementation to pregnant women attending at the Ayder Comprehensive Specialized Hospital. Methods Two hundred pregnant women were recruited in cross-sectional study design between February and April 2018. Results From the total participant pregnant women the urban dweller constituted the major proportion of 182 (91%). Seventy-eight (39%) of the participants had two antenatal care visits, whereas only, 21 (10.5%) of them had an antenatal care visit three and above. One hundred fifty-five (77.5%) participants women had knowledge about the cause of anemia in pregnancy. In this study, 143 (71.5%) of the pregnant women started their iron folate supplement in the second and third trimester. The adherence of iron folate intake was 10.5%. Healthcare education and counseling about iron-folate supplementation (AOR =4.55, 95% CI =[1.534, 13.512]), number of pregnancies (AOR =6.941, 95% CI =[1.511, 31.09]), and number of antenatal visit (AOR =0.242, 95% CI =[0.069, 0.852]) were significantly associated with adherence to iron-folate supplementation. Conclusion Time to start iron folate supplement in the first trimester was low and the adherence level was also very poor, which can be attributed by the number of antenatal care visits, frequency of pregnancy and healthcare education and counseling about iron folate supplement.