[18F]Fluoroethoxy trimethoprim ([18F]FE-TMP, [18F]2), a unique antagonist of bacterial dihydrofolate reductase (ecDHFR), has been developed as a reporter gene imaging agent. Here, we developed new PET probes based on TMP. Simulations predicted that hydrophobic interactions around the benzene ring of 2 contributed to binding with ecDHFR. The more lipophilic fluoropropyl-TMP analog (3) showed a higher binding affinity for ecDHFR than 2. However, 18F-labeled 3 ([18F]3) underwent 18F-defluorination during PET imaging of ecDHFR-transfected mice. Subsequently, we evaluated FE-d4 analog (5) as a candidate exhibiting greater in vivo stability than 2. Metabolite analysis showed a lower contamination of radiolabeled metabolites in mouse brains with 18F-labeled 5 ([18F]5) than [18F]2. PET imaging with [18F]5 of a non-human primate brain was characterized by a distinct signal/noise ratio, which allowed in vivo visualization of brain circuits expressing the reporter gene, demonstrating the superior potential of [18F]5 as a PET probe for reporter gene imaging of the brain.