McKinlay, the Fulham coach who arrived as O'Neill's deputy at the start of 2012, is a passionate believer in what the former Shamrock Rovers boss is trying to do with his national side.
On paper, a record of one win in 14 matches paints a poor picture of O'Neill's first term, but McKinlay insists the work done outside of the senior fixtures will eventually come good.
O'Neill has thrown himself into the job at all levels, taking a keen interest in grass roots football, player eligibility and the appointment of a number of former internationals, including Jim Magilton and Stephen Craigan, to positions within the Irish FA.
The full benefit of that spade work may come after O'Neill and McKinlay have moved on, but the Scot is convinced it is a crucial aspect of the job at hand.
"Behind the scenes I think Michael has done a really, really good job," said McKinlay, ahead of Friday's friendly in Turkey.
"We knew the infrastructure had to improve and we had to build foundations for now and the future.
"He has had to take decisions and we will now see where that is going to take us.
"I think Michael has done an unbelievable job; he is a highly intelligent and extremely motivated individual.
"Whether or not Michael and I see the benefits of what we are trying to implement isn't something I think about, as long as it stands Northern Ireland in good stead for the future.
"I think the IFA recognise the job Michael is doing with the team and behind the scenes.
"This is a work in progress and hopefully we will continue to improve."
Finishing fifth in World Cup qualifying Group F means O'Neill's honeymoon period is long gone and the results must start to change soon.
And although much of their work has been with a long-term aim in mind, McKinlay expects to see a short-term improvement as well.
"Of course we want instant success on the pitch," he added.
"I am hopeful and confident that can happen and we will hopefully get more points on the board in the next campaign.
"There is a pressure from us. We haven't achieved what we set out to do yet.
"The staff and players thought we finished short of what we deserved and I think there is a general acceptance of that and that we are doing things the right way.
"Ultimately it is about winning games, though, and results are the be all and end all.
"We have to turn our good play into better results.
"I am fed up of being frustrated and the players are exactly the same. Sometimes you just need results."