Owen, who has 24 years of business experience and is a trustee of children's charity Barnardo's, takes over from Mike Dickson, who founded Whizz-Kidz and has been the charity's chief executive for 13 years.
Dickson has been appointed as the charity's first chairman, and will also become a full-time fundraiser for Whizz-Kidz.
Owen, who was chosen from 400 applicants, has been charged with building on the charity's existing success and providing a strategic focus for the future. This will involve increasing the charity's fundraising portfolio and developing a campaigning strategy.
"My experience as a trustee of Barnardo's made me realise that there are so many ways I could be using my business acumen to help other people," said Owen, who ran her own successful software development company employing 40 staff before joining Whizz-Kidz. "Obviously I have a specific interest in Whizz-Kidz because of my personal experiences."
Owen's appointment has been warmly welcomed by the British Council of Disabled People, the national umbrella organisation of disability groups run by disabled people.
"We entirely support this move, and it is an issue that we have long campaigned around," said Andy Rickell, the council's director. "Getting disabled people into high-profile director roles can do nothing but good. We hope that more charities follow suit."
The news follows similar moves by other charities over the past year.
The Limbless Association appointed Diana Morgan, who lost both legs in a train accident in 1990, as chief executive last April. Scope recently advertised for a disabled person to take on the newly created role of director of diversity.
Whizz-Kidz has also appointed Debbie Ladds as director of children's services. She will work closely with Owen to help develop the new strategy.