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The current densities in nowadays electronic circuitry are close to the electromigration threshold that may result in the fracture of circuits due to electromigration, hampering further miniaturization of integrated chips. Flexible electronic devices, which use a flexible material instead of rigid silicon as a substrate, might be prone to fracture problems also due to obligatory mechanical deformation. However, finding the location of fractured nanogaps and in situ repairing such atomic‐scale fractured circuits are currently unavailable. To this end, a method is developed to in situ heal nanogaps as large as 20 nm between metallic electrodes on the polyimide (PI)‐covered substrate via voltage sweeping, which is typically employed to generate nanogaps rather than heal nanogaps. The reconnection of nanoelectrodes is realized only when the underneath PI is treated with oxygen plasma etching. Assisted by X‐ray photoelectron spectroscopy, it is revealed that inductively coupled O2 plasma etching not only changes the surface topography but also changes the chemical binding structure of PI, which in return can be used to immobilize metal atoms migrating along the PI surface to gradually close the nanogap, providing an in situ self‐healing paradigm for repairing the atomic scale fractured circuits.