Carson was born in Detroit, Michigan and was raised by his single mother, Sonya Carson. He struggled academically throughout elementary school, but started to excel in middle school and throughout high school. After graduating with honors from Southwestern High School, he attended Yale University, where he earned a degree in Psychology. He chose to go to Yale because in College Bowl, an old knowledge competition TV program, he saw Yale compete against and defeat many other colleges, including Harvard. Carson wanted to participate in College Bowl, but the program was discontinued. From Yale, he attended University of Michigan Medical School.
Carson's hand-eye coordination and three-dimensional reasoning skills made him a gifted surgeon. After medical school, he became a neurosurgery resident at Johns Hopkins Hospital in Baltimore. Starting off as an adult neurosurgeon, Carson became more interested in pediatrics. He believed that with children, "what you see is what you get, ... when they’re in pain they clearly show it with a frown on their face or when they are happy they show it by smiling brightly."
At age 33, he became the youngest major division director in Johns Hopkins history, as Director of Pediatric Neurosurgery. Carson's other surgical innovations have included the first intrauterine procedure to relieve pressure on the brain of a hydrocephalic fetal twin, and a hemispherectomy, in which a young girl suffering from uncontrollable seizures had one half of her brain removed.
In 1987, Carson made medical history by being the first surgeon to successfully separate conjoined twins (the Binder twins) who had been joined at the back of the head (craniopagus twins). The 70-member surgical team, led by Carson, worked for 22 hours. At the end, the twins were successfully separated and can now survive independently. Carson recalls:
I looked at that situation. I said, ‘Why is it that this is such a disaster?’ and it was because they would always exsanguinate. They would bleed to death, and I said, ‘There's got to be a way around that. These are modern times.’ This was back in 1987. I was talking to a friend of mine, who was a cardiothoracic surgeon, who was the chief of the division, and I said, ‘You guys operate on the heart in babies, how do you keep them from exsanguinating’ and he says, ‘Well, we put them in hypothermic arrest.’ I said, ‘Is there any reason that – if we were doing a set of Siamese twins that were joined at the head – that we couldn't put them into hypothermic arrest, at the appropriate time, when we're likely to lose a lot of blood?’ and he said, ‘No way .’ I said, ‘Wow, this is great.’ Then I said, ‘Why am I putting my time into this? I'm not going to see any Siamese twins.’ So I kind of forgot about it, and lo and behold, two months later, along came these doctors from Germany, presenting this case of Siamese twins. And, I was asked for my opinion, and I then began to explain the techniques that should be used, and how we would