The meeting came after some had refused to meet Mr Jonathan last week.
For months the parents have been asking to see the president and he finally accepted an invitation from Pakistani girls’ education activist, Malala Yousafzai, who liaised with parents.
Now UK-based, 17-year-old Ms Yousafzai survived a Taleban attempt on her life in October 2012 when she was shot in the head on a school bus in Mingora, in the Swat Valley area of north-west Pakistan.
Mr Jonathan had blamed activists of the #BringBackOurGirls campaign for politicising the abductions – from a school in Chibok, in Borno state, north-east Nigeria – and influencing the parents.
Chibok spokesman Lawan Abana said 177 people were in the delegation that met Mr Jonathan. Reporters counted 51 of the 57 girls who had escaped their abductors.
At least 11 of the parents have died since the abductions – seven in a village attack this month and four of heart attacks and other illnesses that the Chibok community blames on the trauma of losing their daughters.
Mr Jonathan was accompanied by his ministers of education and of finance, and his national security adviser.
They walked to a stage above the waiting parents and girls, and journalists were asked to leave. Also present was Kashim Shettima, the governor of Borno state. He has accused Mr Jonathan of not doing enough to save the girls and has claimed Boko Haram fighters are better armed and motivated than Nigeria’s military.
The failure to rescue the girls is an international embarrassment and daily #BringBackOurGirls rallies in Abuja, the capital, to ensure attention for the girls’ plight have irked the government.
Some of the Chibok parents and community leaders have made public statements urging Mr Jonathan to negotiate with Boko Haram. The militant group is demanding a prisoner swap for the girls. So far, Mr Jonathan has refused.
Nigeria’s defence ministry, also criticised for not quickly rescuing the girls, has said it knows where they are being held but fears any military intervention puts their lives at risk.
Boko Haram has increased the number and deadliness of its attacks and this month has been closing in on Chibok, threatening to attack again, say community leaders.
Last week Boko Haram took control of Damboa town, about 12 miles from Chibok, and state officials said more than 15,000 people from the town and nearby villages have fled.
Politics has plagued the abduction furore since the start. Nigeria’s first lady, Patience Jonathan, claimed the kidnappings were a set-up to discredit her husband. She also had two leading #BringBackOurGirls activists briefly arrested.
Mr Jonathan has never before met the parents or the escaped girls, though he has repeatedly said: “My priority is the return of these girls.”
In May, he cancelled a planned trip to Chibok without explanation. Last week he said: “As a father of girls, I stand ready to meet with the parents of our abducted children and the truly brave girls that have escaped this nightmare through the grace of God.”
Boko Haram was founded in 2002. Initially it focused on opposing western education – Boko Haram means “western education is forbidden” in the Hausa language.
It launched military operations in 2009 to create an Islamic state. To date thousands have been killed, mostly in north-east Nigeria and attacks have been launched against the police and a United Nations headquarters in Abuja. Some three million people have been affected by Boko Haram’s activities. It was declared a terrorist group by the US last year.