Krone retired for the first time on April 18, 1999, with a three-winner day at Lone Star Park, near Dallas. She embarked upon a broadcasting career in horse racing. From 1999–2000 she worked as an analyst for TVG Network, then worked as a paddock analyst for Hollywood Park from 1999–2002. She came out of retirement at Santa Anita Park in November 2002. After a good start to the 2003 season, she fractured two bones in her lower back and spent the next four months recovering. She returned to lead the 2003 Del Mar jockeys in purse earnings, then went on to become the first woman jockey to win a Breeders' Cup race when she rode Halfbridled to victory in the 2003 Breeders' Cup Juvenile Fillies at Santa Anita. On December 12, 2003, just weeks after her Breeders' Cup win, she broke several ribs and suffered severe muscle tears in a fall at Hollywood Park Racetrack. Though not fully recovered from her injuries, Krone attempted to come back on February 14, 2004, at Santa Anita Park, but failed to win in three races. She did not ride again; on July 8 of that year, she made a statement in which she did not officially retire, but strongly hinted that she would never race again.
Because of her success in the face of severe injuries sustained while racing, Krone was named by USA Today as one of the 10 Toughest Athletes and was honored with the Wilma Rudolph Courage Award by the Women's Sports Foundation. Krone also had been inducted into the Cowgirl Hall of Fame in Fort Worth, Texas, and is a member of the Michigan Sports Hall of Fame. In October of 2013 she was inducted into the National Women's Hall of Fame in Seneca Falls, N.Y., where she joins such iconic individuals as Eleanor Roosevelt, Rosa Parks, Ella Fitzgerald, Georgia O'Keeffe and Billie Jean King.
In 2001 Krone married Jay Hovdey, executive columnist for the Daily Racing Form. She gave birth to their daughter Lorelei Judith Krone in 2005. (Hovdey also has a son, Ed, from his previous marriage.) Krone remains close to her brother Donnie Krone, father Don Krone, and nephew Danny Kauffman. Her mother, Judi Krone, was an accomplished equestrian who died a few days before Christmas of 1999.