Background Numerous studies have confirmed that 3, 4-Methylenedioxymethamphetamine (MDMA) produces long-lasting changes to the serotonergic system and decreases the density of the serotonin reuptake transporter (SERT). However, amitriptyline (AMI) is a potent neuroprotector that can cause devastating neuropathologic injury. Use of 4-[18F]-ADAM, a SERT-specific radionuclide as a molecular imaging agent, facilitates longitudinal, non-invasive assessment of SERT activity/expression post-MDMA. We used 4-[18F]-ADAM PET imaging to access the longitudinal alteration of SERT binding and evaluate the synergistic neuroprotective effect of MDMA and SERT inhibition by AMI in rat model.Materials and Methods The adult male Sprague–Dawley (SD) rats are grouped into four according to drug administration (Group 1: saline, Group 2: MDMA 10mg/kg i.p., Group 3: MDMA 10mg/kg i.p. with AMI 5 mg/kg i.p., Group 4: AMI 5 mg/kg i.p.). All drugs were administrated twice daily for 4 successive days (Day 1 to Day 4). Post-drug 4-[18F]-ADAM PET scans were performed on day 14, day 21 and day 28 to measure the SERT occupancy/recovery. After the last PET imaging, SERT-positive cells were measured quantitatively using immunochemical staining.Results In response to MDMA treatment regimens, SERT binding was significantly reduced in rat brain. Recovery rate (normalized to baseline) in the MDMA group, at day 14 was 64.34% ± 2.05%, progressively increased to 70.70% ± 3.96% at day 28. Recovery rate in the MDMA group varies based on region-specific. AMI dramatically increased SERT binding in all brain regions, enhancing average ~24% recovery rate at day 14 when compared with the MDMA group (MDMA 64.34% ± 2.05% vs. MDMA+ AMI 87.76% ± 2.98%), reaching 84.38% ± 2.05% at day 28. The immunochemical staining revealed that MDMA treatment reduced SERT immunoactivity densities in all brain regions, whereas AMI markedly increased the serotonergic fiber density after MDMA-induction that confirmed the PET findings.Conclusions Using in vivo longitudinal PET imaging, we demonstrated that SERT recovery was positively correlated with the duration of MDMA abstinence, implying the lower SERT densities in MDMA-induced rats reflected neurotoxic effects, varied region-specific, and reversible. AMI globally accelerated the recovery rate of SERT binding and increased SERT fiber density with possible neuroprotective effects.