The amino acid glutamate is the major excitatory neurotransmitter in the CNS, and excessive activation of glutamate receptors is implicated in neurological disorders. N-Acetyl-L-aspartyl-L-glutamate (NAAG), a peptide neurotransmitter widely distributed in the mammalian nervous system, is hydrolyzed by glutamate carboxypeptidase II (GCPII, also known as NAALADase) to liberate N-acetylaspartate and glutamate. Inhibition of GCPII is hypothesized to achieve neuroprotection by increasing NAAG levels (thus enhancing its neurotransmitter activity and regulatory effects) and decreasing glutamate levels. Building on previous work where a dually acting ligand (4,4′-phosphinicobis-(butane-1,3-dicarboxylic acid)) was designed as an mGluR3-selective agonist and potent GCPII inhibitor, we investigated structures comprising two amino acids joined through a urea linkage (envisaged as a replacement for the central phosphinic acid moiety in the lead compound). A series of symmetrical and unsymmetrical urea compounds were synthesized (via reaction of amino acid benzyl esters with triphosgene followed by deprotection), and their inhibitory activity against rat GCPII (stably expressed in Chinese hamster ovary (CHO) cells) was assayed. Key results include: (S)-Glu-C(O)-(S)-Glu (IC50 47 ± 4.5 nM), (S)-Asp-C(O)-(S)-Glu (IC50 46.1 ± 1.4 nM), and (R)-Cys-C(O)-(S)-Glu (IC50 6.9 ± 0.4 nM) as potent GCPII inhibitors—with (R)-Cys-C(O)-(S)-Glu being 6-fold more potent than (S)-Glu-C(O)-(S)-Glu and comparable to the reference inhibitor 2-PMPA (IC50 5.1 ± 0.6 nM). Structure-activity relationship (SAR) analysis revealed that a urea containing at least one glutamate residue plus a second residue with a carboxyl group and an additional moiety (e.g., thiol or tert-butylthio) is critical for effective inhibition. Neuroprotective effects against NMDA-induced neuronal toxicity were tested using a glial cell-mediated assay: (t-Bu)Cys-C(O)-(S)-Glu and (R)-Cys-C(O)-(S)-Glu produced 69% and 50% protection, respectively, superior to PMPA (25% protection at 1 µM). In conclusion, these remarkably simple urea-based compounds act as potent GCPII inhibitors, offering a new avenue for the rational design of GCPII inhibitors that may lead to effective neuroprotective agents for disorders linked to glutamatergic dysfunction (e.g., stroke).