Mortensen moved from Spain to the United States in the late 1990s to play poker. He won $1,500,000 at the 2001 World Series of Poker (WSOP) Main Event. He defeated a then-record field of 613 players, including a very tough final table that included professional players Mike Matusow (6th), 1989 WSOP Main Event champion Phil Hellmuth (5th), Phil Gordon (4th), and Dewey Tomko (2nd). In the final hand, Mortensen's K♣ Q♣ out-drew and defeated Tomko's A♠ A♥, when Mortensen's hand improved to make a straight.
Mortensen won his second career bracelet at the 2003 World Series of Poker in the $5,000 Limit Hold'em event, earning $251,680. He defeated professional player Mark Gregorich heads-up to win the title.
At the 2006 World Series of Poker, Carlos made three final tables. He finished in ninth place in Event #2 (No Limit Hold'em) winning $71,617. He would once again finish in ninth place in Event #6 (NL Hold 'em) earning him another $73,344. He came up just short of winning his third bracelet in Event #33 (Razz), where he finished runner-up to fellow professional James Richburg earning him $94,908.
Mortensen finished in 10th place in the 2013 WSOP Main Event, being the "Final Table Bubble Boy."
Mortensen is considered to be the last big-name poker professional to win the Main Event at the World Series of Poker. As a result of the poker boom, which ignited itself two years after his win, when Chris Moneymaker won the Main Event, the fields in that tournament have increased exponentially making it extraordinarily more difficult for individual players to maintain consistent success in it. A few other big-name players have made the final table in the post-boom years since his victory, but none of them have managed as of 2016 to win the Main Event.
In 2004, he won the World Poker Tour (WPT) Doyle Brunson North American Poker Championship for $1,000,000. Mortensen won the Season Five World Poker Tour championship event for a $3,970,415 first place prize, his largest tournament cash to date, and his second career WPT title, making him the first player in professional poker history to ever win the World Championship events at both the World Series of Poker and the World Poker Tour.
In 2010, Mortensen won the Season Eight WPT Hollywood Poker Open. With this win, he passed fellow professional Daniel Negreanu for first place on the all-time WPT money list, and tied Gus Hansen for most WPT titles with three.
Mortensen has made the prize money in the World Heads-Up Poker Championship, and was a semi-finalist in the second season of the Poker Superstars Invitational Tournament.
Mortensen had a good run at the 2007 European Poker Tour Main Event in Monte Carlo finishing 11th, going out to Joshua Prager after making a straight on the turn, but defeated by a flush on the river.
In 2006, he and his wife, fellow poker player Cecilia Reyes Mortensen, divorced.
As of August 2017, his total live tournament winnings exceed $12,100,000. His 21 cashes as the WSOP account for over $3,200,000 of those winnings.