Ground subsidence caused by permafrost thawing causes the formation of thermokarst ponds, where organic compounds from eroding permafrost accumulate. We photolyzed water samples from two such ponds in Northern Quebec and discovered the emission of volatile organic compounds (VOCs) using mass spectrometry. One pond near peat-covered permafrost mounds was organic-rich, while the other near sandy mounds was organic-poor. Compounds up to C10 were detected, comprising the atoms of O, N, and S. The main compounds were methanol, acetaldehyde, and acetone. Hourly VOC fluxes under actinic fluxes similar to local solar fluxes might reach up to 1.7 nmol C m−2 s−1. Unexpectedly, the fluxes of VOCs from the organic-poor pond were greater than those from the organic-rich pond. We suggest that different segregations of organics at the air/water interface may partly explain this observation. This study indicates that sunlit thermokarst ponds are a significant source of atmospheric VOCs, which may affect the environment and climate via ozone and aerosol formation. Further work is required for understanding the relationship between the pond’s organic composition and VOC emission fluxes.