Background: Women of reproductive age (WRA) are one of the vulnerable population mostly impacted by anemia and iron deficiency (ID) worldwide. Objective: This study aimed to assess the prevalence of anemia, ID, and iron deficiency anemia (IDA) among WRA in Morocco. Material and Methods: This study included a representative sample of 2,012 non-pregnant women aged 15-49 years covering the entire territory of Morocco. Data collection encompassed socio-demographic information, anthropometric measurements, along with blood samples. Hemoglobin (Hb) concentration, serum ferritin (SF), and C-reactive protein (CRP) levels have been analyzed. Results: The median of SF for the entire population was 27 μg/mL (Interquartile Range (IQR): 12-50 μg/mL), and the mean of Hb was 12.2 ± 1.5 g/dL. Significant differences were observed between urban and rural areas: urban SF median was 24 μg/mL (IQR: 11-45 μg/mL) versus rural 31 μg/mL (IQR: 15-55 μg/mL, p < 0.001), and urban Hb mean was 12.2 ± 1.5 g/dL compared to rural 12.4 ± 1.5 g/dL (p = 0.02). Furthermore, the prevalence of anemia, ID and IDA are consistently high; 34.3%, 29.8%, and 16.4%, respectively, with a significant difference in favor of urban areas. Conclusions: Our findings from this national survey reveal that despite over a decade of implementing flour fortification strategy using electrolytic iron to address iron deficiency in Morocco, anemia, ID, and IDA remain widespread among WRA. Exploring alternative strategies or adopting a different form of iron for fortification could be beneficial in reducing or even eradicating iron deficiency among Moroccan women.