University officials will also be at the talks after student protests began last week sparked by proposed fee increases of between 10 and 12%.
Students from across the country have crammed onto buses and trains to travel to Pretoria to join the march.
The demonstrations have closed some of the country’s top universities.
In a statement on Friday, Mr Zuma acknowledged the “financial difficulties faced by students from poor households”, while reiterating that “university fees are determined by universities independently of government”.
Universities say they need to increase fees to maintain standards, and have been hit by a fall by in government subsidies.
On Thursday, 29 people were charged with public violence amid the biggest student protests to hit the country since apartheid ended in 1994. They have been released from custody, and the case postponed to February.
The demonstrations began last week at Johannesburg’s prestigious University of the Witwatersrand, and have since spread to at least 10 universities, forcing the closure of many of them.
The mainly black students say they cannot afford fee increases and have rejected a government offer to cap increases at 6%, down from the 10% to 12% proposed by the management of universities.
Correspondents say the protests show growing disillusionment with the governing African National Congress (ANC), which took power after minority rule ended in 1994, over high levels of poverty, unemployment and corruption in government.
Many black students say they come from poor families, and fee increases will rob them of the opportunity to continue studying.
Financially better-off white students have joined the protest, mainly to show solidarity with the black students.
Source:BBC
S. African fee protests: President Zuma to meet students
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Thousands of South African students are marching to the capital Pretoria, where President Jacob Zuma is expected to meet their leaders about tuition fees.