From 2009 to 2012 he worked at Airlines Papua New Guinea.
Before Air New Zealand he had served in various positions in Australian carrier Qantas, including as a director, deputy chief executive and chief financial officer.
The 58-year-old faces several challenges as he takes over at the indebted airline, which last month reported a quarterly loss and is trying bed down a deal with Gulf airline Etihad. Etihad bought a 24 per cent stake in Jet Airways two months ago.
Toomey said the fast-growing Indian aviation market "offered significant potential for Jet Airways not only within India, but beyond, through new or improved international connections".
Jet Airways last month posted a wider-than-estimated fourth-quarter loss of US$85 million because of higher aircraft lease costs, high fuel prices, a weak rupee against the US dollar, other exceptional items and a one-time expense.
The airline has a fleet of 100 aircraft and employs close to 14,000 staff.