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One of the major problems currently facing satellite-based positioning is the atmospheric refraction of the GPS signal caused by the troposphere. The tropospheric effect is much more pronounced at the equatorial region due to its hot and wet conditions. This affects the GPS signal due to the variability of the refractive index, which in turn affects the positional accuracy, especially in the height components. This paper presents a study conducted in the Southern Peninsular Malaysia located at the equatorial region, to investigate the impact of tropospheric delay on GPS height variation. Four campaigns were launched with each campaign lasting for three days. The Malaysian real-time kinematic GPS network (MyRTKnet) reference stations in Johor Bahru were used. GPS RINEX data from these stations were integrated with ground meteorological data observed concurrently from a GPS station located at the Universiti Teknologi Malaysia (UTM), at varying antenna heights for each session of observation. A developed computer program called TROPO.exe based on the Saastamoinen tropospheric delay model was used in estimating the amount of tropospheric delay. The result reveals that, there is inconsistency in the delay variation, reaching maximum delay of 18 m in pseudo-range measurement. The height component shows variations with a maximum value of 119.100 cm and a minimum value of 37.990 cm. The result of the simulated data shows 5.00 m of differences in height gives an effect or improvement of 1.3 mm in signal propagation. This indicates that, tropospheric delay decreases with increase in antenna height.