Background: Children's health is very important for their better learning and timely nourishment everywhere in the world. Malnutrition among school going children has remained a big challenge in under developed countries. Methods: Cross-sectional study was conducted among 422 children of four Government Primary schools of Qasimabad, district Hyderabad after taking the proper consent and administration approval from the head of school. Multi stage simple random sampling technique was adopted. Study was approved from Institutional review board of Health Services Academy Islamabad. Results: Out of total, 217 (51.4%) were boys and 205 (48.6%) were girls. Mean Height of boys and girls were 128.09 cm (±SD 12.90) and 130.36 cm (±SD 12.50) respectively. Mean Weight of boys was 25.27 Kgs (±SD 6.17) while in girls mean Weight was 26.83 Kgs (±SD 7.03). 17.57 cm (±SD 2.34) was mean MUAC for all participants and mean BMI was 15.42 (±SD 2.02). Prevalent of stunting and wasting were 24.4% and 18.3% respectively. While in 13.7% thinness (BMI for age) was seen. Stunting was statistically significant in girls 9-10 year (p value=.015, CI: .118-.823, OR=.311) and 11-≥12 years (p value=.018, CI: .215-.874, OR=.434). Pallor was more in girls (17%) and Dental caries were higher in boys (20.8%). Insufficient breakfast was done by 347 (82.2%), whereas 75 (17.8%) were doing sufficient breakfast. 341 (80.8%) students became ill during last year, out of that 80 (19%) were having history of hospitalization. Conclusion: Poor polices and lack of food aid interventions regarding health of primary school going children was assessed during this study.