ObjectiveThe main objective of this study was to explore the factors affecting anaemia among women of reproductive age (WRA) in Nepal using spatial and multilevel epidemiological analysis.DesignThis cross-sectional study analysed data from the 2016 Nepal Demographic and Health Survey. Spatial analysis was performed using ArcGIS software V.10.8 to identify the hot and cold spots of anaemia among WRA (15–49 years). Data were analysed using multilevel mixed-effect logistic regression analysis.SettingNepal.ParticipantsA total of 6414 WRA were included in the analysis.Main outcome measureAnaemia defined by WHO as haemoglobin level less than 120 g/L in non-pregnant women and less than 110 g/L in pregnant women.ResultsThe spatial analysis showed that statistically significant hotspots of anaemia were in the southern Terai region (four districts in province 1, eight districts in province 2, one district in Bagmati province, two districts in province 5 and one district in Sudurpaschim province) of Nepal. At the individual level, women who underwent female sterilisation (adjusted OR, aOR: 3.61, 95% CI 1.10 to 11.84), with no education (aOR: 1.99, 95% CI: 1.17 to 3.39), and from middle socioeconomic class families (aOR: 1.65, 95% CI: 1.02 to 2.68) were more likely to be anaemic, whereas, older women (>35 years) (aOR: 0.51, 95% CI: 0.26 to 0.97) and those women who were using hormonal contraceptives (aOR: 0.63, 95% CI: 0.43 to 0.90) were less likely to be anaemic. At the community level, women from province 2 (aOR=2.97, 95% CI: 1.52 to 5.82) had higher odds of being anaemic.ConclusionWRA had higher odds of developing anaemia, and it varied by the geographical regions. Nutrition-specific and nutrition-sensitive interventions can be tailored based on the factors identified in this study to curb the high burden of anaemia.