The 48-year-old guided Al-Merrikh to four wins, two draws and two losses in his eight matches in charge leaving his side in second place in the Sudanese Premier League, two points adrift of league leaders Al-Hilal with a game in hand.
However, Clark handed in his resignation over the weekend and that has been accepted by the Red Devils' board.
A club statement read: "The journey of our boss Lee Clark with us comes to an end after he resigns as head coach of our club and the Board of Directors announces its acceptance of the resignation.
"Thank you, Lee. We wish you the best in your next step."