Rooney (48), who is also a director of Montecillo veterans' home, the chairman of the the RSA Welfare Trust and a trustee of the Otago Therapeutic Pool, has accepted a job with the Civil Aviation Authority and is moving to Wellington.
He will be replaced by an acting chairman who is yet to be appointed.
Rooney said after seven years on the board he was going to retire anyway, so his new job in Wellington had simply moved the process forward by a few months.
The union's annual meeting takes place in early March - when a new chairman will be elected - and the appointments panel interviews candidates just after Christmas for prospective board members.
Rooney, who was employed as an engineer with the Royal New Zealand Air Force for 20 years before going into the private sector, said it had been a challenging couple of years and this year especially had been tough.
''We knew this year, in particular, was going to be a challenging year,'' he said.
''We've got a new rental agreement over the venue hire and a couple of major sponsorships who came on board when we were struggling a few years ago are now coming up for renewal.''
The union does not host a test at Forsyth Barr Stadium this year, which also hits it in the pocket.
''But we always knew this year was coming and we have planned accordingly.''
The union had recorded good profits in the past two years - adding up to more than $500,000 - and had started banking some reserves.
Rooney took over from Doug Harvie, who is now chairman of the Highlanders.
The union has been undergoing a strategic review for most of the year and Rooney said it was not far off being signed off by the board.
The review looked into the delivery of rugby right across the province and where it needed to improve and what was missing.
''What you might need in Dunedin may be totally different than what is needed in Owaka or in Queenstown,'' he said.
He said the gaps appeared to be in coaching and, more specifically, in coaching coaches.
''We do not think we use assets that we have here in the region well enough. Talented players and people who finished their playing careers are just left alone. We don't engage with these people enough.''
He said perhaps there were people focused on activities rather than outcomes.
''We might get people ticking off that they have been to a school three times a year. But perhaps they should be looking at how many more people they got playing the game from their visits.''
He said the union did not appearing to be putting too many resource into any particular part of the game.
Some people had commented the union was placing a large emphasis on rippa rugby but he was comfortable where it sat and was good for the development of the game.
The deputy chairman of the board is Keith Cooper but no indication has been given on who would take over as acting chairman.
Rooney said it was a great result by Otago against Southland on Saturday and had been done through plenty of hard work.
Rooney said he would enjoy now just watching the game rather than riding every result so hard.
''You get used to thinking that missed tackle will cost us $50,000 or this kick will be worth $20,000. Now I'll be able to just enjoy the game for what it is.''
