Anas Sarwar, who has often spoken about his commitment to social justice, is not using state primaries and has opted for Glasgow's £8234-a-year Hutchesons' Grammar.
The SNP's John Wilson criticised the move.
Sarwar, 30, is one of Scottish Labour's rising stars. He was elected MP for Glasgow Central in 2010, voted deputy leader the following year and is Labour's referendum co-ordinator. He is also tipped to be party leader one day.
Since entering politics, Sarwar has promoted his social justice credentials, writing: "I don't think it's acceptable we ignore the inequalities that are happening today because the only change on offer is a constitutional one."
However, his personal commitment to "world-class public services" has been questioned after it emerged he was not using a state school for his own son.
Sarwar recently sent his son to "Hutchie", an exclusive independent school which he also attended and where fees range from £8234 a year for primary pupils to £10,230 for secondary education.
Pupils at the secondary tend to achieve far better grades than the children at local comprehensives.
Across Scotland, fewer than 5% of children are educated in the private sector.
Sarwar's move highlights the pitfalls for Labour politicians, who are the most vocal in their support for state schools, when making schooling choices for their children.
In the 1990s, the then Labour leader Tony Blair was criticised after he sent his son to the grant-maintained London Oratory School.
Labour MP Harriet Harman also had to defend her decision to opt for a grammar school.
In Scotland, senior Glasgow councillor Stephen Curran was criticised after it emerged his children were being educated privately. He is currently the administration's executive member for education and young people.
Bob Thomson, Labour's former treasurer in Scotland, said: "If the political party you represent supports state education, you should support it in practice. If a lot of politicians are not sending their children to state schools, then there is not the same level of involvement in trying to improve state schools."
MSP John Wilson said: "Anas Sarwar once again highlights the hypocrisy of the Labour Party - talking of social justice and defending public services while sending his own child to a private school.
"The deputy leader of the Labour Party in Scotland should talk the talk and use the education system provided by his own Labour administration in Glasgow."
A Scottish Labour spokesman said: "This is a private matter for Anas and his family."