Significance Whereas tissues can repair wounds regularly, single cells—including muscle cells, neurons, and cancer cells—are increasingly recognized to have a wound response. Ability to understand and control single-cell repair holds the potential for new strategies to treat human diseases. Existing wounding methods and model organisms are insufficient for elucidating the biological mechanisms involved. This paper reports a microfluidic guillotine for the high-throughput bisection of hundreds of cells reproducibly. The fine time resolution achieved enables mechanistic studies critical for a molecular understanding of single-cell wound repair currently impossible with existing wounding methods. The work here will lay the foundation for understanding how single cells heal themselves, a fundamental feature distinguishing living from nonliving matter.