The midfielder was an unused substitute in last night's Europa League thriller against Anderlecht.
Mourinho claims Herrera and utility man Ashley Young are the only two 'fresh' players in his squad.
A number of first-team regulars including Zlatan Ibrahimovic, Marcos Rojo, Chris Smalling and Phil Jones are currently injured.
Mourinho believes United are 'in trouble' and hinted that reserve team skipper Axel Tuanzebe could be involved at Turf Moor.
“Eric Bailly has played six matches in a row – 540 minutes in a row,” Mourinho said.
“We lost Marcos Rojo, we don’t have Jones, we don’t have Smalling.
“We are in trouble and, now, we lose Zlatan too but, in attack, we have options: Rooney is coming and let’s see if Mata can also return before the end of the season. Let’s see what happens.
“Herrera plays [against Burnley]. He didn’t play on Thursday – one yellow card and he would have missed the semi-finals.
“I was thinking about him and [fellow substitute Marouane] Fellaini both at the same time but, because I made a change with Marcos Rojo, I couldn’t do that and he didn’t play.
“So Herrera is fresh to play. Ashley Young is fresh to play and who else? Nobody else is fresh to play!
“Now we need absolutely everyone and I don’t have to think about Axel Tuanzebe going to the Under-20 World Cup in Korea because maybe Axel has to come now. We need everybody.”
Herrera scored in United's 2-0 win against Chelsea last weekend.
