The charge relates to an incident while Levein was in his director of football role and attending an Under-18 derby clash between Hearts and Hibs at the Oriam.
The nature of the incident is unknown, but Levein will face a hearing at the national stadium on Wednesday April 17.
He is charged with breaching Disciplinary Rule 207 - “No official shall commit Misconduct at a match.”
Levein has already had one trip to Hampden over discipline issues after comments he made in the aftermath of a 2-1 defeat to Rangers, suggesting that he felt Hearts were “playing against 13 men”.
The Hearts boss was hit with a two-match ban, with one suspended.