With skipper Steven Gerrard missing due to suspension and Frank Lampard ruled out with a knee injury, the honour has fallen to the striker for one game at least. Lampard may yet return to the squad for Tuesday's fixture away at Poland.
Rooney has won 76 caps since making his debut in 2003, scoring 29 times for the national side. He has captained England just once before, in a friendly against Brazil in Doha in 2009.
"It is a great honour," he said in a press conference on Friday. "It is something I am really proud of and it is a big challenge for myself.
"It's something I am really looking forward to and hopefully we can cap the day off with a good victory."
With 98-time international Ashley Cole the subject of disciplinary proceedings following an offensive tweet last week the defender was unlikely to take the armband, though he remains available for selection.
Manager Roy Hodgson was giving little away regarding his team selection, but he did say he was pleased to have Rooney a the helm.
"I haven't spoken to the players about the team, but I guess Wayne Rooney knows he is starting the game as he is sitting alongside me as captain of the team," he said.
"He will back me up when I say that I haven't told any other players who will be playing and who won't be playing, so I'm afraid that although I've got a pretty good idea in my own mind what I'm going to do, I can't divulge that until I've spoken to the players.
"It might be a question of utilising the squad in a different way, as we have an important game in Poland on Tuesday but all of my thoughts this week have been on how best to use the squad knowing that really, whichever team I choose, we will rightly be able to win this game.
"How many players I will spare and keep fit and fresh for the game on Tuesday is the decision that has to be made and one that I've given a lot of thought to.
"I am really pleased about that (having Rooney back) and I've enjoyed working with Wayne. We were at the Euros and I enjoyed working with him there and it was a big disappointment when he got that terrible gash which we thought would keep him out of the October games.
"But luckily he made a very quick recovery and now he's available to captain the team in the first game."
San Marino are one of only three teams with zero rankings points in FIFA's standings and have conceded 473 goals in 114 internationals. Rooney says England have to ensure they avoid focusing on their opponents' lowly status as they look for an impressive win ahead of a much trickier trip to Warsaw on Tuesday.
"I think we have to focus on ourselves and play the kind of football we have been trying to do," he said. "We have been working hard all week and the manager has been trying to put across to us all what he wants of us and expects of us and we to try and make sure we do the best we can and put the training sessions into the game."
Wembley has sold out in anticipation of a flurry of goals and Rooney praised England fans for showing such enthusiasm despite the poor quality of the opposition.
"The fans, certainly since I have been involved for England, have been fantastic," he said, "following us all around the world and to have 90,000 fans there tomorrow is fantastic for the players.
"We are looking forward to the game and hopefully we can put on a show for the fans."
- Wayne Rooney