The council is urging parents of children due to start primary school this September, to enrol them by January 15.
Parents of four-year-olds, born between September 1, 2013 and August, 31 2013 have to apply by the January deadlines or they will be considered late applicants.
This could mean their application is not considered until June.
The two January deadlines for applications are January 13 for paper applications and January 15 for online applications.
Each parent is able to choose four schools but no parent is guaranteed a place, even if other siblings are at the preferred school.
Councillor Zoe Nolan, said: “We have really good primary schools in Milton Keynes.
“The standards have continued to rise and I want to make sure that parents are able to have their choice of school.
“That is why applying by the 15 January is so important. I would urge every parent to apply before the closing date.”
April 18 is national ‘offer day’ - when parents receive school place offers, but only if they have applied before the deadline.
Cllr Nolan added: “If any parents are finding the application process difficult they should either e mail or telephone the council where advice and help can be given.
“Whatever challenges parents face I would ask them to get in touch as soon as possible so we can help them to apply.”
For more information, contact the education access team on: firstname.lastname@example.org