The parents were left in disarray when their children were allocated secondary school places at Bishop Young Academy or Leeds East Academy, up to nine miles away from their homes in south Leeds.
While the council has now allocated 60 additional places at Cockburn School in Beeston, the parents say they will keep campaigning until all 66 young people are guaranteed a place at their local schools.
Parents and supporters gathered at St George's Centre at 11am to put their concerns to Leeds Central MP Hilary Benn, Middleton Park Councillor Paul Truswell and Councillor Jonathan Pryor, Leeds Council's Executive Member for Learning, Skills and Employment.
The campaigners called for action to reassess the 'failing' school admissions system in Leeds, to look at the realignment of school clusters and to introduce safeguarding policies for children travelling by public transport to school.
Charlotte Wharton, 31, was 'devastated' when her son was allocated Bishop Young Academy, about nine miles away from her home in Middleton.
Her son Charlie would need to travel an hour and a half by bus to school, followed by a 15 minute walk in an unfamiliar area.
Charlotte, a call centre manager, said: "It was devastating for both of us. He's nervous about the journey and he's angry, because all his friends have got Cockburn.
"It's a safeguarding issue, our control over our own children is being taken away.
"How can I say to him that he can't go into town on a Saturday with his friends, if he's being sent all that way to school? It's not fair.
"They're still kids, he rarely walks to school on his own which is over the road, let alone to Leeds city centre and up the other side of Leeds at 7am in the dark."
Concerns were raised that more housing is being built across Middleton, despite there being no secondary school in the immediate area.
While the new places at Cockburn School came as a relief to parents, Charlotte is concerned the problem will only worsen in the future.
The mum-of-two added: "We have another little boy who isn't due to go into secondary for years, but if they don't sort it out we'll have the same problem with him too.
"It's not going to go away."
MP Hilary Benn said it was 'unacceptable' that some children in his constituency would have to travel so far to attend school.
Addressing the protest, Mr Benn said: "There is clearly a problem about insufficient places here at Middleton Park in particular and in south Leeds.
"The council wanted to open the new school in 2018 and if it had been opened we would have averted this crisis."
The Lawrence Calvert Free School was unable to open its doors as planned in September 2020 due to circumstances 'outside the council's control'.
Cllr Pryor reassured the parents that with the 60 new places at Cockburn School and others likely to become available, there should be about 75 additional places at south Leeds schools to accommodate the 66 young people affected.
But he admitted that schools in Leeds are 'bursting' and could not keep expanding to provide extra places.
Cllr Pryor said: "In many cases, the nearest school with free places has been Seacroft - which is ridiculous.
"It shows how full and bursting at the seams our schools are, because it means every single school from here to Seacroft is completely full.
"That's how few places there are and that's exactly why we have created more places."
Cllr Pryor added that in south Leeds alone, 1,500 more school places have been created by Leeds Council since 2016.
"While there are 66 young people affected this year, if we hadn't had done that there would have been 1,500 of you stood here today", he said.
"I completely accept we had more work to do and we weren't quite there, but I think that gives some perspective on how big the issue is."
Parents and carers have until March 16 to register to be on the waiting list for schools.
Places will begin to be offered at schools where there are now vacancies, including the additional places at Cockburn School, from March 23.