HIV-1 protease inhibitors (PIs) are the most potent class of drugs in combinational antiretroviral therapies (cART). However, the current therapies are still not adequate due to the emergence of drug resistance. There is still a need for development of more potent PIs. The objective of this study was to search for multi-drug resistant inhibitors to combat HIV-1 and viral resistant proteases. Our lab developed a fission yeast (Schizosaccharomyces pombe) cell-based system that allows large-scale or high-throughput drug screening. We first used a cell growth-based assay to test a drug candidate. We then used a HIV-1 enzymatic assay to confirm it. We explored four batches of potential anti-HIV compounds as well as nine FDA approved PIs. All FDA-approved PIs potentially inhibited HIV-1 PR with 3 small molecule compounds showed minimal inhibitory effects. Results of this study demonstrated the use of fission yeast cell-based system as a means to discover new PIs.