PI3KC2α is a phosphoinositide 3‐kinase with a recently reported function in platelets; PI3KC2α‐deficient mouse platelets have altered membrane structure and impaired function. Yet, how these membrane changes cause platelet dysfunction remains unknown. Here, focused ion beam‐scanning electron microscopy of PI3KC2α‐deficient platelet ultrastructure reveals a specific effect on the internal membrane structure, while liquid chromatography‐tandem mass spectrometry profiling of 294 lipid species shows unaltered lipid composition. Functionally, PI3KC2α‐deficient platelets exhibit impaired thrombosis specifically under conditions involving membrane tethering. These studies indicate that the structural changes in PI3KC2α‐deficient platelets are limited to the membrane, occur without major changes in lipid composition, and selectively impair cell function during thrombus formation. These findings illustrate a unique mechanism that may be targetable for anti‐thrombotic benefit.