Background High dietary salt intake is recognized as a risk factor for several non-communicable diseases (NCDs), in particular cardiovascular diseases (CVDs), including heart attack and stroke. Accurate measurement of population level salt intake is essential for setting targeted goals and plans for salt reduction strategies. We used a spot urine sample to estimate the mean population salt intake in Nepal and evaluated the association of salt intake with excess weight, hypertension, raised blood sugar and hypercholesterolemia, and a number of socio-demographic characteristics. Methods A population-based cross-sectional study was carried out from February to May 2019 using a WHO STEPwise approach to surveillance. Spot urine was collected from 4361 participants aged 15–69 years for the analysis of salt intake. We then used the INTERSALT equation to calculate population salt intake. Student’s ‘t’ test, one-way ANOVA and multivariable linear regression were used to assess the association between salt intake and a number of factors. Statistical significance was accepted at P < .05. Results The average (±SD) age of participants was 40 (14.1) years. Mean salt intake, derived from spot urine samples, was estimated to be 9.1g/d. A total of 70.8% of the population consumed more than the WHO’s recommended amount of 5g salt per day, with almost one third of the population (29%) consuming more than 10g of salt per day. Higher salt intake was significantly associated with male gender (β for male = 0.98g; 95%CI:0.87,1.1) and younger age groups (β25–39 years = 0.08; 95%CI:-0.08,0.23) and higher BMI (β = 0.19; 95%CI:0.18,0.21). Participants who were hypertensive and had raised blood cholesterol consumed less salt than people who had normal blood pressure and cholesterol levels (P<0.001). Conclusions Salt consumption in Nepal is high, with a total of 70.8% of the population having a mean salt intake >5g/d, well above the World Health Organization recommendation. High salt intake was found to be associated with sex, age group, education, province, BMI, and raised cholesterol level of participants These findings build a strong case for action to reduce salt consumption in Nepal in order to achieve the global target of 30% reduction in population salt intake by 2025.