The present study evaluated the concentration, seasonal variations, source identification and health risk through inhalation of heavy metals (V, Cr, Mn, Fe, Ni, Cu, Zn, As, Cd, Si and Pb) in fine particulate matter. Samples of PM2.5 were collected from an urban site in Agra (27°10′N, 78°05′E), India during January 2018 to January 2019. A total of 48 samples of PM2.5 were collected using Fine Particulate Sampler (Envirotech APM 550) set at a flow of 16.6 L min− 1 on 47 mm quartz fiber filters (Pallflex, Tissuquartz) for 24 h. Heavy metals were determined by Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) after acid digestion. The average PM2.5 mass concentration was 107 ± 57.85 µg m− 3 which has been compared with NAAQS and WHO limit was found to be higher. Seasonal variation of PM2.5 showed: winter > post-monsoon > summer > monsoon. The average concentration of heavy metals lied within the range of 4.92 to 505.38 ng m− 3. Among heavy metals, the high concentration belonged to Si (505.38 ng m− 3) and Fe (281.23 ng m− 3). The highest metal concentration occurred in the winter season followed by post-monsoon, summer and monsoon seasons. The enrichment factor was used to estimate the main sources of the metals in PM2.5. Two factors were identified using Principal Component Analysis (PCA) at the urban site including resuspended road dust, vehicular activities, solid waste incineration, industrial emission and construction activities. To assess the health risks through inhalation exposure pathway hazard quotient (HQ), hazard index (HI) and carcinogenic risk (CR) were estimated. The carcinogenic risks of Pb (for both children and adults) Cd (for children) were lower than the precautionary criterion (1×10− 6), while Cd for children and As, Cr and Ni for both children and adults were higher than 1×10− 6. The non-carcinogenic risks of As, Cd, Cr, Mn and V for both children and adults were lower than the safe level of 1, whereas Ni for both children and adults were higher than the safe level of 1. The HI values of all heavy metals for both children and adults were higher than the safe level of 1 indicating a non-carcinogenic adverse health effect. The results of the present study impart information for the behaviour and risk mitigation of heavy metals.