Although the NutriPlus program has shown considerable evidence of enhancing users’ nutritional status, the budget does not cover all eligible mothers and children. This study aimed to conduct a cost-benefit analysis of the NutriPlus program to assess its economic efficiency. 53 families with 79 users in the NutriPlus program at Daejeon Dong-gu Health Center participated in this study with informed consent. The costs and benefits were estimated from both the administrator’s and users’ perspectives. We converted the time cost into Korean currency based on the minimum wage in 2014. The value of nutrition education and service (B2), estimated by contingency valuation method (CVM), was counted as an economic benefit. 6 families (11.3%) were recipients of national medical care and 22 families (41.5%) paid 10% of the food package cost by themselves. The total cost was 7,450,167 and the total benefit was 12,402,239. The budget for the health center (C1+C2+C3+C4) was 5,984,381 a month. Time and transportation cost for receiving nutrition education (C6) differed significantly according to the economic status of families. Household food consumption increase (C4-B4) was 40,379 in the poverty group, which was four times more than in the other groups. The net benefit (B-C) was 4,852,172 and the B/C ratio was 1.66. Therefore, the NutriPlus program is beneficial in the economic aspect as well as in the nutritional aspect. If the enhancement of nutritional status was also considered, the total benefit would be even higher. These results confirm the legitimacy of a secure budget for the NutriPlus program. And we suggest expanding its budget to cover more eligible individuals to improve people’s health and welfare.