In 2003 Carroll joined the staff of Baseball Prospectus, for whom he served as its injury expert and wrote a regular "Under the Knife" column and periodic "Team Health Reports" as well as hosts Baseball Prospectus Radio. In February 2009, he assumed the role of Executive Editor of Puck Prospectus. In September 2010, Carroll announced his departure from Baseball Prospectus and published his last "Under the Knife" column. Two days later, writing on his own blog, he gave a partial explanation:
I left Baseball Prospectus — and let me be very clear: I left — for a number of reasons, but the most significant is that I have impossibly high standards for my work. I’m wrong a lot. It’s the nature of what I do, but each instance burns me. There was an episode this summer where it was clear the goals of the organization and the goals I had didn’t mesh any more. I can’t say any more about that, but it was the final straw for me and at that point, I began the process of leaving. In the end, I bought myself out of the contract and sold back the equity I had earned in the company. It was a better option for me not to write at all than continue to write there.
In 2006, Carroll served as the injury expert for the short-lived The Fantasy Show on ESPN.
Starting in 2007, Carroll has worked as an NFL injury expert for SI.com. He has also served as a Senior Writer for Football Outsiders, for whom he focuses on football injuries.
Carroll has authored three books:
Saving the Pitcher (2004),
The Juice: The Real Story of Baseball's Drug Problems (2006), and
The Carroll Guide to Sports Injuries (2010).