The reigning Eredivisie champions have renewed the young left-back's contract, even though he has managed just 14 appearances in the past 15 months for the club
The new deal means that the 20-year-old, who has struggled for fitness over the course of the past year, will be at the club for four more years, having impressed boss Frank de Boer and his coaching staff in the brief moments he appeared for the Dutch champions last season.
"Nicolai left a big impression on us in those few matches and many training sessions, and he still does," De Boer told Uefa.com.
Boilesen also spoke of his delight at agreeing renewed terms with Ajax, and feels it has made all of his efforts to recover from his setbacks worthwhile.
"This is fantastic," said Boilesen. "This is the highlight of my recovery. Luckily I am progressing in the right direction. I train very hard twice a day. I only think positive now."