"We are confused and devastated," the Semmy Foundation, the charity organisation supported by six-year-old Tjin, announced on its Facebook page.
It said he died on the final day of a new fund-raising drive, without specifying when.
Diagnosed with a rare form of brain cancer in May last year, Tijn fired the public's imagination when he launched a move to dare people to paint their nails, hoping to raise a few hundred euros.
"Paint your nails, make a donation and then challenge three of your friends to do the same," his donation page said at the time.
Within a few days, his action netted more than 2.5 million euros (S$3.9 million), with numerous public figures including Dutch Prime Minister Mark Rutte and DJ Armin van Buuren donning nail polish in support.
In total, more than nine million euros were collected and the Dutch press hailed the brave youngster as a superhero. Soon he became known as "SuperTijn".
Pope Francis in April blessed him in a letter sent from the Vatican City after he was told about the nail polish initiative.
Before his death, Tijn was working on a new charity drive called "Lak door Tijn" (Dutch for "Nail polish by Tijn") in which he sold four colours of polish to collect money to buy a specialised machine to treat children with brain cancer.
The goal amount of one million euros was reached on Thursday night, Dutch media reported.
His family was flooded with condolences and the hashtag #tijn became the top trending topic on Twitter in The Netherlands, even uniting opposing Dutch politicians in their grief.
"Rest softly, young brave hero," far-right politician Geert Wilders tweeted, with a picture of him sporting bright red nails during the original charity drive.
"Thank you for your inspiration, little big man," tweeted Mr Jesse Klaver, leader of the leftist Green Party (GL).
Mr Rutte praised him for inspiring people.
"Tijn is an example for many," he said before the boy's death.