But Hill had been hampered by ankle injuries ever since his arrival in Orlando, playing in only four games in his first season with the Magic, 14 games in his second and 29 in his third. He was forced to sit out his entire fourth year with Orlando (2003–04). Meanwhile, the Pistons, who had defeated the Magic in the 2003 Playoffs but ended up losing to the New Jersey Nets in Eastern Conference Finals, won the championship the following year in 2004.
In March 2003, Hill underwent a major surgical procedure in which doctors re-fractured his ankle and realigned it with his leg bone. Five days after the surgery was performed, Hill developed a 104.5 °F (40.3 °C) fever and convulsions. He was rushed to a hospital. Doctors removed the splint around his ankle and discovered that Hill had contracted a potentially fatal methicillin-resistant Staphylococcus aureus (MRSA) infection. He was hospitalized for a week and had to take intravenous antibiotics for six months.
The 2004–05 season saw a return to the old Grant Hill, who was so popular earlier in his career. Hill, though hampered by a bruised left shin that caused him to miss several games, started and played 67 games for the Magic, well over the combined amount of games he played for the Magic the previous four seasons. He was named the Eastern Conference player of the week for the week between November 15–21, 2004. Over the season, Hill averaged 19.7 points per game on a .509 field goal percentage. Fans voted him an All-Star starter again, and he led the Eastern Conference All-Star Team to a victory over the West. In addition, at the conclusion of the season, Hill was awarded the Joe Dumars Trophy presented to the NBA Sportsmanship Award Winner.
During the 2005–06 season, Hill was once again injured frequently as nagging groin injuries kept him sidelined for much of the first half of the season, limiting him to 21 games. He got a sports hernia that was caused by an uneven pressure on Hill's feet while he was running, due to concerns that he could re-aggravate the injury on his left ankle if it got too much pressure. Hill underwent surgery for the hernia and has since stated that he would consider retirement if he has to get another surgery.