Computer aided fragment-based lead discovery has been successfully applied to the design of inhibitors of aspartyl protease enzyme β-secretase (BACE1). A benzimidamide fragment, which binds to the two catalytic aspartic acid residues in the active site of the enzyme, was selected as the starting compound. A novel series of 3-phenethylbenzimidamide inhibitors were designed and synthesized. Although biological evaluation results showed that the compounds displayed poor inhibitory activity towards BACE1, 3-phenethylbenzimidamide analogs might be modified as potential BACE1 inhibitors.