Jim Duffy, aged 52, currently head of the denominational St Cadoc's primary, has been seconded by East Renfrewshire Council as acting head of the 222-pupil Calderwood Lodge Jewish primary school in Newlands, Glasgow.
It is the only state faith school outside the Catholic sector.
The move follows the retirement of Ruth Levy as head of Calderwood Lodge and comes at a critical point in the school's future because of its falling roll. It has a capacity for 290 children, including nursery pupils.
A spokesman for the council said that, despite advertising widely north and south of the border for a Jewish headteacher, it had been unsuccessful.
With only half a dozen Jewish schools in the whole of the UK, the bulk of them in London and Manchester, recruitment had been difficult, he said.
Dr Duffy's appointment coincides with a campaign by the council to boost the roll at Calderwood Lodge. The school faces competition from the independent sector for Jewish youngsters and the Jewish community in East Renfrewshire is an ageing one.
Younger families tend to move out of the area, either to London or Australia because of better employment prospects. There has also been a trend for Jewish parents to remove their children from Calderwood Lodge at P7 stage and put them into independent schools, rather than the associated secondary, Mearns Castle High.
"It could become critical if people don't see Calderwood Lodge as their first port of call," the council spokesman said.
The council is to issue leaflets jointly with the organisation Calderwood Jewish Education telling Jewish families: "Calderwood Lodge is your school - make sure you support it."
Dr Duffy is used to spanning theological divides: he is a former head of St James's primary in Paisley which formed half of MossvaleSt James primary school, one of Scotland's first shared campus primary schools.
John Wilson, director of education at East Renfrewshire, said the Jewish education authorities were content that the school's faith and and ethos would be protected by a head from another faith school.
The difficulties facing the school follow concerns which have been expressed about staffing difficulties in Catholic schools and about finding teachers for Gaelic schools. Critics fear it could also become an issue if Muslims in Scotland were successful in establishing their own schools.