The meeting comes as the United States upped the pressure on Ortega's leftist administration by imposing visa restrictions on police and other officials linked to the deadly unrest.
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"The political violence by police and pro-government thugs against the people of Nicaragua, particularly university students, shows a blatant disregard for human rights and is unacceptable," US State Department spokeswoman Heather Nauert said in a statement.
Nauert did not name the individuals but said they included national police and health officials, along with others at the local level -- "those directing or overseeing violence against others exercising their rights of peaceful assembly and freedom of expression."
The Nicaraguan Center for Human Rights said 134 people had been killed in the violence since protests started on April 18.
"We have counted 134 deaths until Thursday," the center's secretary Marlin Sierra told AFP.
The dead included four young people killed late Wednesday in clashes between pro- and anti- government groups in the towns of Chinandega and Nueva Guinea.
Press reports said an armed group of pro-government supporters had attacked students who were attempting to block traffic heading to the Honduran border.
The Roman Catholic Church has agreed to act as mediator to try to resolve a crisis that began with protests against social security reform but later blossomed into widespread rejection of Ortega, who has been in power continuously since 2007.
However, bishops called off the talks last week after a crackdown on a protest led by victims' mothers left at least 16 people dead. It said they would not resume until the government ends the repression.
Bishops proposed meeting
But the Nicaraguan Episcopal Conference said Wednesday in a statement that after listening to "various sectors" both in the central American country and abroad, the bishops had proposed the new meeting and Ortega had accepted.
"We asked the president... for an audience to discuss the essential and urgent issues of our country, justice and democracy, which peace depends upon, with the goal of evaluating the viability of continuing the dialogue," a statement said.
"We are confident that they can convince Ortega to have a much more open attitude," said a student protest leader at the National Autonomous University, which has been leading opposition to the leftist leader.
Thursday's meeting will be held at the government's convention center in the capital Managua and be followed by a press conference at 7:00 pm (0100 GMT Friday).
Carlos Tunnermann, who is representing civil society in the stalled, broader talks with the government, said he hoped Ortega would seriously commit to negotiations.
On Tuesday, the general assembly of the Organization of American States approved a declaration "in support with the people of Nicaragua," which urged Ortega and Nicaraguans alike to engage in constructive dialogue to address the crisis and prevent further violence.
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