Zinc deficiency, a common malnutrition in children and women is a global public health problem.Burden of zinc deficiencyis more in countries with low meat and high cereal food consumption like Nepal. Nationally representative data on zinc status in Nepal is lacking at present. This study analysed the data from the recent Nepal National Micronutrient status survey 2016(NNMSS-2016) to determinethe prevalence of zinc deficiency and associated risk factors among children aged 6-59 months (n=1462) and non-pregnant women aged 15-49 years(n=1923) from three ecological zones, Hill, Terai, and Mountainof the country. Venous blood was collected from the participants to measure micronutrients such as zinc, markers of anaemia, vitamin A, and markers of inflammation. Stool was collected to assessthe soil-transmitted helminths (STHs) and Helicobacterpylori infection. Socio-demographic, household and other relevant information were collected by a structured questionnaire. Logistic regression was used to examine the predictors of zinc deficiency among the participants.The overall zinc deficiency in children was found to be 22.9% while it was higher in non-pregnant women (24.7%). Predictors associated with zinc deficiency among enrolled children in the study were,living in rural areas (AOR=2.25, 95% CI, [1.13, 4.49]),occurrence of diarrhoea during the two weeks preceding the survey (AOR=1.57, 95% CI, [1.07, 2.30]), household wealth quintile (AOR= 0.48, 95% CI,[0.25, 0.92]) and vitamin A status (AOR=0.49, 95% CI,[0.28, 0.85]. Risk factors associated with zinc deficiency among the non-pregnant women were being underweight (AOR=1.60, 95% CI,[1.15, 2.23]), fever occurrence during two weeks preceding the survey (AOR=1.45, 95% CI,[ 1.06, 1.99]), H. pylori in the stool (AOR=1.32, 95% CI, [1.03, 1.70]), being rich (AOR=0.64, 95% CI,[0.42, 0.98]) and being in the risk of folate deficiency (AOR=0.60, 95% CI,[0.37, 0.96]). We conclude that community focused intervention programs including health and nutrition counselling and livelihood opportunities focusing groups at high-risk may improve the zinc status in Nepal.