Predicting ionospheric Total Electron Content (TEC) variations associated with seismic activity is crucial for mitigating potential disruptions in communication networks, particularly during earthquakes. This research investigates applying two modelling techniques, Autoregressive Moving Average (ARMA) and Cokriging (CoK) based models to forecast ionospheric TEC changes linked to seismic events in Indonesia. The study focuses on two significant earthquakes: the December 2004 Sumatra earthquake and the August 2012 Sulawesi earthquake. GPS TEC data from a BAKO station near Indonesia and solar and geomagnetic data were utilized to assess the causes of TEC variations. The December 2004 Sumatra earthquake, registering a magnitude of 9.1–9.3, exhibited notable TEC variations 5 days before the event. Analysis revealed that the TEC variations were weakly linked to solar and geomagnetic activities. Both ARMA and CoK models were employed to predict TEC variations during the Earthquakes. The ARMA model demonstrated a maximum TEC prediction of 50.92 TECU and a Root Mean Square Error (RMSE) value of 6.15, while the CoK model predicted a maximum TEC of 50.68 TECU with an RMSE value of 6.14. The August 2012 Sulawesi earthquake having a magnitude of 6.6, revealed TEC anomalies 6 days before the event. For both the Sumatra and Sulawesi earthquakes, the GPS TEC variations showed weak associations with solar and geomagnetic activities but stronger correlations with the earthquake-induced electric field for the considered two stations. The ARMA model predicted a maximum TEC of 54.43 TECU with an RMSE of 3.05, while the CoK model predicted a maximum TEC of 52.90 TECU with an RMSE of 7.35. Evaluation metrics including RMSE, Mean Absolute Deviation (MAD), Relative Error, and Normalized RMSE (NRMSE) were employed to assess the accuracy and reliability of the prediction models. The results indicated that while both models captured the general trend in TEC variations, nuances emerged in their responses to seismic events. The ARMA model demonstrated heightened sensitivity to seismic disturbances, particularly evident on the day of the earthquake, whereas the CoK model exhibited more consistent performance across pre- and post-earthquake periods.