Towering striker has been restricted to just one Premier League appearance so far this season.
West Ham are just a point above the relegation zone.
Mkhitaryan, 27, set up two goals in United's 4-1 win over the Hammers in the EFL Cup.
Rooney is one short of Sir Bobby Charlton's all-time United record of 249 goals.
United beat West Ham 4-1 in EFL Cup quarter-final on 30 November.
The two sides played out a 1-1 draw in the Premier League on Saturday.
Paul Pogba and Marouane Fellaini are both suspended after picking up fifth bookings.
Manchester United and West Ham United face each other in the EFL Cup quarter-final clash at Old Trafford.
Spain international feels United will go on a winning run sooner rather than later.
Portuguese boss has until 6pm on Thursday 1 December 2016 to respond to the charge.
Mourinho was sent off for the second time this season.
Michael Carrick reportedly picked up an injury before West Ham United clash.
Mourinho sees red for the second time this season as United falter at home again.
Payet signed a long term contract with West Ham last February.
Manchester united have not in their last three home games.
The 21-year-old spoke to many people behind the scenes at United before making his decision.
West Ham boss insists he does not fear the sack despite his side sitting just one point above the bottom three.
Harry Kane scores a dramatic late brace as Mauricio Pochettino's unbeaten side halt a seven-match winless run.
Hammers boss suggests club might look at 'one or two' players.
Toby Alderweireld, Erik Lamela and Ben Davies not available for Saturday.
French midfielder recently admitted that he was not closing the door to anything following PSG rumours.
Sampaoli did, however, label midfielder as an 'intelligent footballer who any coach would want to have'.