A vehicle diagnostics clearing system that detects a clear diagnostic faults flag and clears diagnostic faults from a control module includes a clear diagnostic faults flag monitoring module and a clear diagnostic faults module. The clear diagnostic faults flag monitoring module periodically monitors the clear diagnostic faults flag in the control module. When the clear diagnostic faults flag monitoring module detects that the clear diagnostic faults flag is set, the clear diagnostic faults module clears the diagnostic faults from the control module for a predetermined period.