For the first time, a member of the Church of Scotland, Morag McCreadie, will take over the running at St Joseph's Primary in Selkirk and St Margaret's Primary in Hawick.
Ms McCreadie, 37, depute head at Drumlanrig Primary in Hawick, is on a temporary one-year contract and will be known as a "manager of learning" rather than headteacher. She will be supported by a principal teacher in each primary, responsible for their Catholic dimension.
The decision had been taken, said Mr McGrath, because of the Scotland-wide shortage of headteachers. Catholic schools had "an even smaller pool of talent to draw from", he pointed out.
In future, however, the Catholic Church plans to tackle headteacher shortages by encouraging teachers in promoted posts to be "more ambitious" and targeting potential leaders early. At one time, according to Mr McGrath, headship would have been seen as the "automatic next step". But now staff were questioning if the pay and additional responsibilities were worth it.
The Borders appointment was "a response to a particular situation" and would not be part of their new strategy - although he acknowledged that "situations can change".
Mr McGrath continued: "Clearly our preference would be to have a headteacher responsible for all areas of the school. What's been arrived at here is a compromise."
According to the Association of Headteachers and Deputes in Scotland, the average number of applications for each headteacher post has dropped from 5.4 in 2002-05 to 4.9 in 2005-08, with 35 per cent of headteacher jobs having to be re-advertised over the past three years. This showed the lack of appeal for headship and the lack of quality in those who do apply.
"These issues need to be investigated. They back up the importance of the research going on into the recruitment and retention of headteachers," said Mr Dempster.
Last week, The TESS revealed how Scottish Borders Council plans to deal with the shortage by merging eight to 12 schools and replacing them with four to six larger ones, and increasing the number of shared headships so that all heads are non-teaching. Currently, seven headteachers run more than one school: this is to be extended to just 42 heads managing 65 primaries.
The EIS, however, argued that "there should be a headteacher for every school". Shared headship, they claimed, leads to problems with workload and stress.