McNally, 40, joins the club with immediate effect ahead of Saturday’s EVO-STIK League West Division game at home to Mossley.
He said: "I am joining a fantastic club with a great history & tradition. At the moment the club isn’t in the best position in the league but we will work very hard as a club to improve this, I am looking forward to it.”
McNally’s main coaching experience to date came with Cammell Laird, where he was assistant, and then at their phoenix club Cammell Laird 1907, who he helped secure automatic promotion in their first season in the North West Counties league.
Club Secretary Daniel Roberts added: "On behalf of the board of directors, I am delighted to welcome Paul McNally to Skelmersdale United.
“Paul is an ambitious young Manager and his vision and ambitions match that of the club, Paul has been consistently successful in his managerial career to date achieving promotions in his last two assignments and we are sure that he will be very successful at Skelmersdale United too."
McNally succeeds Dave Powell, who left the club earlier this week.