Introduction: The high prevalence of chronic energy deficiency (CED) and anaemia among pregnant women in Indonesia is worrying. Nusa Tenggara Timur (NTT) is one of the provinces in Indonesia with the highest prevalence of CED. This study aimed to determine the effect of fortified milk supplementation on changes in mid-upper arm circumference (MUAC) and haemoglobin level among pregnant women. Methods: This quasi-experimental study was conducted in three locations of Community Health Centers in NTT from May to August 2019. Purposive sampling was used to recruit 69 pregnant women who were divided into two groups based on haemoglobin levels; the intervention group consisted of 31 pregnant women with haemoglobin levels below 11 g/dL, and control group consisted of 38 pregnant women with haemoglobin levels above 11 g/dL. Intervention group was provided with fortified milk supplementation, while control group received education about prevention of CED and anaemia. Data were analysed using regression discontinuity design with haemoglobin of 11 g/dL as cut-off. Results: Using regression discontinuity method, we were able to determine the effect of milk supplementation based on haemoglobin levels and confirm the result that milk supplementation significantly increased MUAC by 4.69 cm. Despite no discontinuity found, a positive increase of 0.98 g/dL in haemoglobin level was important to note. Conclusion: Milk supplementation of 300 kcal/day for three months significantly increased MUAC and to some extent, increased haemoglobin level. Thus, it should be considered when planning nutrition programmes to improve the nutritional status of pregnant women.