Muller takes the reins from Ireland hooker Rory Best, and could still play a part in South Africa's World Cup campaign having been called into the extended Springbok training camp.
But the 31-year-old, who has won 23 caps for his country, withdrew from the squad to face Australia in the Tri-Nations after suffering a hamstring injury.
And Muller, who signed a one-year extension to his contract at Ravenhill, remains philosophical about his chances of going to New Zealand.
He said: "If I don't get picked for South Africa again, if I don't get picked for the World Cup that's fine with me, I've got a great challenge ahead over here especially with the captaincy, however, if I do get a call up that would be fantastic, and I would be honoured to go to another World Cup and play another game for my country. Whichever comes my way I'm a true believer that everything happens for a reason."
Any disappointment in not making Peter De Villiers' squad is tempered by his pride at being handed the Ulster captaincy.
"It's obviously a great honour for me and I'm really excited and looking forward to a great challenge in 2011-12," he added.
"I think it's going to be a much tougher season, a lot of pressure and a lot responsibility as well and I'm excited about that.
"I enjoy the leadership role. Rory has done an outstanding job as captain and if I can do as good a job as he has over the past four years then I'll be a very happy man.
"As a captain you only run at the front, there's plenty of leaders in the side, plenty of guys who can make call and captain the side on any given day so for me, it's just about running at the front and making sure the backs make the right calls! I'm really excited and hugely honoured by it."
After an impressive recruitment drive last summer that saw the likes of Muller and compatriots Pedrie Wannenburg and Ruan Pienaar arrive at Ravenhill, Brian McLaughlin's side duly delivered a credible third-place finish.
However Muller is adamant the club won't be resting on their laurels as they target success in both the RaboDirect Pro 12 and Heineken Cup.
He said: "It's going to be a much tougher challenge for us this season, partly because of the World Cup but also because last season people didn't really expect us to do well and we surprised them.
"If we want to be a successful side, and a side that can compete in the future with any side in Europe then we need to be better this year than last year, not just in the quarter-finals and semi-finals but every single week and in every single thing that we do, on and off the field.
"The big challenge not only for me as captain but the whole squad, the management and coaching staff is to make the step up."
63x46.png){kind=logo}