The academies, which started after the summer holidays and are based in Falkirk and Edinburgh, cater for boys and girls in S1. Each follows a different model: one is based in a school and football becomes part of the curriculum, while training at the other academy takes place in the evenings. Both, however, benefit from expert coaching and will run for two years, during which time they will be evaluated by academics from Stirling University, with a view to extending the best approach throughout Scotland.
"The academies have to be evaluated to within an inch of their lives so that in two years' time we can say: 'this is what you need to run it nationally'," says Neil Mackintosh of the SFA's football development department, who is leading the programme.
Falkirk's football academy is based at Graeme High. In May and June, the selection process began, with 49 young people participating in trials, including five girls - nine boys were selected. "The process was rigorous. Parents were making decisions about education," Mr Mackintosh said. "We needed to be sure we were picking the right children."
The boys spend six periods a week receiving coaching from experts such as former Celtic and Dundee United defender Mark McNally. It is his job to equip them with the technical, physical and psychological tools needed to thrive.
If the programme has a negative impact on the youngsters' school work, it will be deemed a failure. "If our programme does not fit in with school and affects their education positively, it does not matter if we turn out footballers," Mr Mackintosh added. "It has to do both."
Meanwhile in Edinburgh, the SFA is working in conjunction with the city's Sports Academy to train 12 boys and 16 girls two days a week after school.