Seizure control (SC) is often poor in cases of magnetic resonance imaging- negative epilepsy after resection surgery. This study aimed to evaluate the therapeutic efficacy of depth-electrode-guided stereotactic radiofrequency thermocoagulation (RFTC) applied to the amygdalohippocampal complex (AHC) for the treatment of patients with MRI-negative medial temporal lobe epilepsy. A total of 62 cases with magnetic resonance imaging-negative medial temporal lobe epilepsy were retrospectively studied after the application of depth-electrode-guided RFTC to the AHC. Single-target coagulations were applied to all patients, and multi-target coagulations were applied to those patients who did not experience significant reductions in discharges after the first target ablation. Bilateral-target coagulations were applied to bilateral medial temporal lobe epilepsy patients, using single target ablation applied to each side. After 24-83 months of follow-up, 32/62 (51.61%) patients became seizure-free, and 35/62 (56.45%) patients reported significant reductions in seizure episodes. The total effective rate was 69.35% (43/62). No significant differences were observed for SC among the single-target, multi-target, and bilateral-target groups. However, a significant difference was observed for the reduction in epileptic discharges after coagulations between those patients who became seizure-free and those who did not. Magnetic resonance imaging-negative medial temporal lobe epilepsy patients can benefit from RFTC applied to the AHC. A significant reduction in epileptic discharges observed during operations after RFTC is applied may predict good SC. RFTC applied to the AHC could be considered a promising method for the treatment of magnetic resonance imaging-negative medial temporal lobe epilepsy patients.