Law enforcement sources said the 20-year-old suspect was under guard at an undisclosed Boston hospital.
Fox News reported that the suspect suffered severe burns.
It was not immediately clear why the man was hospitalized and whether he was injured in the attack or in his apprehension.
The man was caught less than two hours after the 2:50 p.m. bombing on the finish line of the race, in the heart of Boston.
NY AUTHORITIES RAMP UP SECURITY AFTER BOSTON EXPLOSIONS
PHOTOS: EXPLOSIONS ROCK BOSTON MARATHON
In addition, Boston police have surveillance video of someone bringing multiple backpacks to the blast site, according to CBS News.
Police also confirmed that there was a third explosion, at the John F. Kennedy Presidential Library and Museum. It was not immediately clear how much damage was done or whether it was related to the bombings at the marathon finish line.
The library bombing occurred about 4:30 p.m. and more than a mile from the marathon.
A law enforcement source confirmed to The Post that 12 people were killed and nearly 50 were injured in today's blast.
Source: New York Post