Abstract The NavIC (Navigation with Indian Constellation) system’s performance degrades significantly in equatorial low latitude region due to ionospheric effects. Ionospheric scintillation (IS) is one of the major problems to NavIC system. IS occurs due to the random fluctuations in amplitude and phase of the signal. It also depends on solar cycle, latitude, seasons, time and elevation angle of the satellite. Not much significant amount of work is reported on ionospheric scintillation effects on NavIC signals. In this paper, ionospheric scintillation effects on NavIC L5 band (1176.42 MHz) and S1 band (2492.08 MHz) signals due to (1B,1C,1D,1E,1F,1G) are investigated. Amplitude scintillation index S4 is computed based on Carrier to Noise ratio (C/N0) measurements from ISRO IGS (IRNSS/GPS/SBAS) receiver for Kurnool station (Lat:15°47′49″N, Lon:78°4′39″E) and Hyderabad (Lat:17°23′31″N, Long: 78°19′10″E) station. The analysis is carried out for Kurnool station (June and September months) and Hyderabad station for Equinox Months (March & September) and Solstice Months (June & December) for the year 2017. IS effects of L5 and S1 band signals are analysed. It is observed that scintillation effects are severe for L5 band compared to S1 band signals. This work will be helpful to improve the user position accuracy.