The International Global Navigation Satellite Systems (GNSS) and the South African ground based network of dual frequency Global Positioning System receivers provide a unique chance to monitor the space weather effects on the ionospheric total electron content (TEC) over South Africa. In particular, using the University of New Brunswick ionospheric modelling software, TEC was computed over collocated HRAO (27.69°E, 25.89°S) ASTECH X-ZII3 and HARB (27.71°E, 25.89°S) TRIMBLE 4000SSI GNSS receivers located at Hartebeesthoek for the solar X17 flare which occurred on day 301, 2003 and the recent solar X9 flare which occurred on day 339, 2006. TEC values were compared by computing the TEC differences between these stations for the two selected flares. It was found that the TEC difference between HRAO and HARB is large (~9 TECU) for the X17 flare compared to the X9 (~6 TECU). The possible reasons for the TEC difference between the two receivers could presumably be attributed to the receivers’ instrumental differences, inaccuracy associated with the single-layer ionospheric model, and inaccuracy within the geometric mapping function. Furthermore, a comparison of the TEC values over South Africa for these flares show evidence of solar cycle dependence. This is important for future application in high frequency radio communication, navigation, positioning, frequency management and long term studies of impact of solar outputs on climate change over South Africa.