Using vertical total electron content (VTEC) data that were derived from the Malaysia Real Time Kinematic GPS network (MyRTKnet), we analyzed the time variation of the VTEC with the occurrence of medium-scale traveling ionospheric disturbances (MSTIDs) based on ionospheric pierce point (IPP) trajectories. MSTIDs are known as ionospheric disturbance phenomena that generally induce perturbations in important ionospheric parameters such as the ionospheric total electron content (TEC). A method was developed to detect the existence of MSTIDs by identifying rapid fluctuations in the TEC by subjecting the TEC data time series to high-pass filtering. Data were evaluated using the GPS MyRTKnet network over Peninsular Malaysia in the month of September 2007 (a time period with relatively low geomagnetic activity). Two-dimensional maps over Peninsular Malaysia were constructed based on the IPP trajectories. Analysis of the cross correlation of detrended VTEC data from six MyRTKnet stations (PASP, KRAI, GMUS, CAME, TLKI and SBKB) yielded MSTID velocities of around 100 ± 50 m s−1 in the daytime and 60 ± 30 m s−1 in the nighttime, with occurrences of 17.6% and 13.7%, respectively. The results show that although the MSTID wave structure propagates southwestward, some waves also move northward. These waves were connected to the effect of the meridional neutral wind in the upper regions of the ionosphere (400 km).