The girls were kidnapped from the Government Secondary School, Chibok on April 14, about a year after the president declared a state of emergency in the state to curtail the Boko Haram insurgency.
About 217 of the girls are still with their kidnappers after others escaped from the insurgents.
While it took the president almost a month to speak publicly on the kidnap, he is yet to visit Chibok and is yet to meet with the parents of the teenagers, despite local and international condemnation of the government's actions and inactions.
However, on Monday, Mr. Jonathan declared he would finally meet with the parents of the victims.
He also promised scholarships for all the abducted school girls in any part of the country when they return home.
The President stated these when he received Malala Yousafzai, a Pakistani school pupil and education activist from the town of Mingora.
Malala was shot by a Taliban gunman in 2012 for championing girl-child education and has been a promoter of the cause since she survived the attack.
Malala, who is in Nigeria on the commemoration of her 17th birthday, told journalists during a briefing after the meeting that Mr. Jonathan promised her that he would meet with the parents of the abducted girls as well as ensure that they are returned home safely.
Briefing journalists alongside the president's spokesperson, Reuben Abati; her dad, Ziauddin Yousafzai; and the Director of Operations of Malala Foundation, Eason Jordan; the Pakistani teenager said she is in Nigeria to support girls' education and advocate for the release of the Chibok girls.
July 14 is Malala Day, a day set aside by the United Nations for the world to focus on putting all girls in school.
She said she met with parents of some of the girls the previous day and they had expressed the longing to meet with the President and anybody who can help them find their girls.
"I am here in Nigeria on my 17th birthday for a price which is to see that every child goes to school," Malala said. "This year, my objective is to speak up for my Nigerian sisters about 200 of them who are under the abduction of Boko Haram and I met the president, Goodluck Jonathan, for this purpose."
"I convey the voice of my sisters who are out of school or who are still under the abduction of Boko haram. And for those girls who escaped from the abduction but still do not have education. And in the meeting, I highlighted the same issues which the girls and their parents told me in the past two days. The parents said they really want to meet with the president to share their stories with him. And I asked the president that if he wants to meet with the parents of the girls, the president assured me that he would meet with them," she said.
She added that the parents of the girls "still have this hope that there is still someone who can help them. They asked me if there is any chance for them to meet the president because at this time, they need the president's support. I am hopeful that these two promises, the return of the girls from Boko Haram and meeting with their parents, will be fulfilled and we will see it soon".
Malala also told journalists that the Malala fund had raised $200,000 "and we want to use it to contribute to those children's education. We have started working with two organisations here in Nigeria to be able to help these girls continue their education".
The teenage activist, who noted that having as much as 10.5 million children out of school in Nigeria was not encouraging as some of these children can end up as terrorists or being violated, also urged the president to increase the budgetary funding for the education sector.
"If Nigeria must have a bright future, every child must have an opportunity to go to school," she said.
The Director of Operations of Malala Foundation also told journalists that Mr. Jonathan said to Malala that "he can guarantee that all the girls that have been kidnapped including the ones that escaped will be given scholarships to go to school in other parts of the country".
Malala said from her interaction with the president, she deduced that he is pained by the girls' situation who he described as his own daughters and was feeling the pains of their sufferings.
"The president has expressed his solidarity with those girls and his sadness. He has assured that these girls will come back home safely. He has several options but that he will choose the best to ensure the girls are released safely," she said.
At the briefing, Mr. Abati said the president used the opportunity of the meeting to take Malala through some of the programmes being carried out by the federal government.
He mentioned the Presidential Initiative for the North East, an economic recovery programme that the federal government has embarked upon with collaboration of state governments in the north east; and the Safe School Initiative which has already been launched with an initial $10 million fund.
He added that Mr. Jonathan emphasised his commitment to making sure that schools are safe, every child enjoys right to education and that that right is no way violated by anyone.
Mr. Abati said the president also announced that he would this week launch the Victims Support Fund for victims of terror and a committee will be set up in partnership with state governments, civil society, and other stakeholders.