Applications are submitted through Studielink, the national portal. Not every institution admits applicants from abroad through it: some run a procedure of their own, and that is checked before any preparation begins.
The deadlines apply nationally. Programmes with a limited number of places (numerus fixus) accept applications until 15 January; all others until 1 May. Selection for numerus fixus programmes runs from 15 January to 15 April, and an applicant may apply to no more than two such programmes in an academic year. A place that is offered has to be accepted in Studielink within two weeks, or it passes to the next candidate.
Universities may set earlier deadlines for applicants from outside the EU, in part because the immigration procedure takes time once a place is offered. The calendar is therefore built around the specific programme rather than the national date.
An applicant does not apply for the residence permit themselves: the university submits the application to the immigration service, provided it is listed as a recognised sponsor. The entry visa and the residence permit are then requested in a single procedure.