She will be the first woman to have run the Royal Opera House, and the first woman to lead any one of the four great national companies - the Royal Opera House, English National Opera, Royal National Theatre and the Royal Shakespeare Company.
Few women have risen to the top in the arts administration in Britain, though large numbers of women work in arts companies. On the artistic side too, it is unusual to find high-profile international female directors such as Deborah Warner.
It is significant, however, that Ms McIntosh will not have the title of general director, enjoyed by Sir Jeremy Isaacs, nor will she have his remuner- ation. Her pounds 90,000 salary will be pounds 24,000 less than Sir Jeremy's and she will not have artistic control of the Royal Opera and Ballet companies, although their directors, Nicholas Payne and Anthony Dowell, will report to her.
Keith Cooper, spokesman for the Royal Opera House, said the board had wished to distinguish between the artistic management and the "huge" job of running the organisation.
Ms McIntosh's departure from the National opens up another round of musical chairs as a replacement will have to be found for her. That replacement will work alongside the new artistic director of the National, Trevor Nunn, who succeeds Richard Eyre next year.
Among likely candidates to replace Ms McIntosh in running the financial, administrative and production side of the National are Ruth McKenzie, director of the Nottingham Playhouse, Nick Starr, a former senior producer at the National who has left to run Warwick Arts Centre, Mary Allen, secretary general of the Arts Council, and Carole Winter, West End producer and former senior executive with the English Shakespeare Company.
Ms McIntosh, who will join the Royal Opera House later this year, several months before Sir Jeremy retires, will find it a hotter potato than the National which has enjoyed artistic acclaim, relative financial stability and good labour relations in the past few years.
At the Royal Opera House more than 200 people will be made redundant when the House closes down for two years next summer. There is still a substantial financial deficit, and controversy over high ticket prices and the pounds 78m lottery award for redevelopment.
Jenny McIntosh, as she is known, is 49. Before working at the National she was casting director and controller of planning at the Royal Shakespeare Company. Her ex-husband, Neil McIntosh, was director of Shelter and of Voluntary Service Overseas. She lives in north London with her two children.
Sir Angus Stirling, chairman of the Royal Opera House board, said: "The board is delighted to have found in Jenny McIntosh a successor to Sir Jeremy Isaacs who has exactly the right blend of artistic and managerial experience to lead the Royal Opera House through the forthcoming years of redevelopment and change."
Ms McIntosh said that the artistic reputation of the Royal Opera and the Royal Ballet had never been higher and she looked forward to "the challenge of seeing the Royal Opera House through an invigorating period of change, into a new era in a new house".