Chemical proteomics studies the effects of drugs upon cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus proteome analysis at single cell level is needed. So far, single cell proteomics techniques have not been quantitative enough to tackle the drug effects on the target proteins. Here, we developed the first single cell chemical proteomics (SCCP) technique and studied with it the time-resolved response to anticancer drugs methotrexate, camptothecin and tomudex of individual adenocarcinoma A549 cells. For each drug SCCP identified and quantified 1,000-2,000 proteins across >150 single cells in a time course of treatment up to 48 h, revealing the early emergence of cellular subpopulations committed and uncommitted to death. SCCP represents a novel approach to exploring the heterogeneous response to drugs of cancer cells.