Electromagnetic stimulation (EMS) has proven to be useful for the focal suppression of epileptiform activity (EFA) in the hippocampus. There is a critical period during EFA for achieving the transition from brief interictal discharges (IIDs) to prolonged ictal discharges (IDs), and it is unknown whether EMS can modulate this transition. Therefore, this study aimed to evaluate the intensity- and time-dependent effect of EMS on the transition of EFA. A juvenile rat EFA model was constructed by perfusing magnesium-free artificial cerebrospinal fluid (aCSF) on brain slices, and the induced EFA was recorded using a micro-electrode array (MEA) platform. After a stable EFA event was recorded for some time, real-time pulsed magnetic stimulation with low and high peak-to-peak input magnetic field intensities was carried out. A 5-min intervention with real-time magnetic fields with low intensity was found to reduce the amplitude of IDs (ID events still existed), whereas a 5-min intervention with real-time magnetic fields with high input voltages completely suppressed IDs. Short-time magnetic fields (9 s and 1 min) with high or low input intensity had no effect on EFA. Real-time magnetic fields can block the normal EFA process from IIDs to IDs (i.e., a complete EFA cycle) and this suppression effect is dependent on input intensities and intervention duration. The experimental findings further indicate that magnetic stimulation may be chosen as an alternative antiepileptic therapy.