MP Makhosi Khoza has repeatedly called for Mr Zuma to resign. Last week, she said he was a disgrace.
She has received death threats warning her to stop pushing for a secret ballot when MPs vote on Mr Zuma next month.
Parliament and the police decided to provide security for her.
Last week, the ANC said she had crossed the line and must face disciplinary action for speaking out against the president.
The ANC in her home province of KwaZulu-Natal called her comments a "blatant betrayal of the core values" of the party.
Ms Khoza, 47, has also been a critic of corruption within the ANC.
Mr Zuma has faced numerous allegations of corruption, all of which he denies.
The National Assembly is expected to vote on a motion of no-confidence in him on 8 August.
Milton Nkosi, BBC News, Johannesburg
The decision to charge Makhosi Khoza with "ill-discipline" is the best example of how the ANC is shooting itself in the foot. Following its disastrous performance in last year's local government elections, the party promised to "self-correct".
But what the South African electorate is witnessing is the ANC inflicting wounds on itself that might not heal in time for the next general election due in 2019.
Ms Khoza is a PhD MP and one of its most popular out of the over 200 in the National Assembly.  She is being punished for speaking truth to power.
This is exactly what Nelson Mandela warned South Africans about his party's impunity when he said: "If the ANC does to you what the apartheid government did to you, then you must do to the ANC what we did to the apartheid government."
The ANC seems like an unstoppable train rattling downhill at break-neck speed. If there was ever an example of when the 105-year-old party needed to apply the brakes it is here. But the people are likely to punish these leaders in two years' time.
Last week Ms Khoza received a death threat saying she had 21 days left to live.
She called Mr Zuma a disgrace at a ceremony to mark Nelson Mandela's birthday on 18 July.
She was addressing civil society groups, unions and business leaders pressing for Mr Zuma's removal in next month's  no-confidence vote.
There is no suggestion that he is connected to the death threats.
Jacob Zuma has survived several previous votes of no-confidence.
The constitutional court ruled in June that parliament had the right to conduct a secret ballot, but the speaker has yet to announce a decision on the issue.
Mr Zuma is due to stand down as ANC president in December and whoever takes over would lead the party into the 2019 elections.
An outspoken member of South Africa's African National Congress (ANC) party has been charged with ill-discipline for speaking out against President Jacob Zuma.