CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single gene knockout phenotypes can be masked by redundancy among related genes. To address this issue we developed pgPEN, a pooled CRISPR-Cas9 single and double knockout approach targeting over 2,000 human paralogs. We applied pgPEN to two cell lines and discovered that 12% of human paralogs exhibit synthetic lethality in at least one context. We recovered known synthetic lethal paralogs MEK1/MEK2, important drug targets CDK4/CDK6, and other synthetic lethal pairs including CCNL1/CCNL2. These findings nominate drug targets to help expand targeted therapy options for cancer.