Background: Food security refers to accessing to desirable, nutritious, and healthy foods to live a healthy and productive life. Household food insecurity is an underlying cause of malnutrition in children. In this study, the household food security and its influence on the nutritional status of under-five year children were investigated. Methods: A cross-sectional analytical study was conducted from August to November 2019 in Syangja district of Nepal. Of six rural municipalities of the district, Phedikhola Rural Municipality was selected using the lottery method. We found 905 eligible households that have an under-five year child. A total of 289 children entered the study after considering the 40% overall prevalence rate of malnutrition among children under five years of age.  Data were collected proportionately from each ward considering the health status and anthropometric measurements of children and household food security using a structured interview schedule and the Household Food Insecurity Access Scale. Descriptive statistics and chi-square tests were applied to assess the situation and determine the association. Results: Food insecurity was observed in more than half (52.3%) of the households. Food insecurity was associated (P < 0.001) with the socioeconomic status of the family. Prevalence of stunting (height-for-age), underweight, and wasting (weight-for-height) in children were 28.7%, 20.0%, and 13.9%, respectively. Food security, exclusive breastfeeding, and initiation time of complementary feeding were significantly associated with wasting and underweight (P < 0.05). Conclusion: Food insecurity and under-five year malnutrition were highly frequent in the study areas. The improvement of educational, occupational, and economic conditions of the households may be a solution to this problem