"Truly inspiring to be able to come here. Anne was a great girl. Hopefully she would have been a belieber," Bieber wrote, according to the museum's Twitter and Facebook accounts.
The pop star's swarms of fans refer to themselves as "Beliebers."
A person close to the singer told ABCNews.com that Bieber spent more than an hour touring the museum and learning about Anne, who was fond of pop culture and hung pictures of celebrities on her bedroom walls.
Annemarie Bekker, spokeswoman for The Anne Frank House, said the pop star is "a fan of Anne and maybe Anne would have been a fan of his."
"We think he meant it well. He's only 19 years old and living in a crazy world … with all girls being fans of him worldwide. Maybe that is also why he wrote it down," she said of the pop star's guestbook entry.
The day after Bieber's visit, The Anne Frank House posted the singer's guestbook entry on its Facebook page, where reaction was swift. The post garnered thousands of comments, most of them negative.
"She would've been a WHAT?," wrote one user. "That little idiot is way too full of himself. She's an important historical figure so show some respect."
"Way to turn an inspiring moment into something about yourself," wrote another.
"I beliebe this kid is justin idiot," another non-"Belieber" wrote. PHOTOS: Justin Bieber Through the Years
Bieber was in The Netherlands for a Saturday night concert in Arnhem.
The Frank family went into hiding in 1942, after the Nazi occupiers of The Netherlands issued an order for Anne's sister Margot to be arrested and sent to a concentration camp. The family lived in an unused and isolated part of the building above Otto Frank's business, which they called the Secret Annex. They were joined by four other people and relied on the support of Frank's employees to bring them food and necessities during the war.
Anne, who was 13 years old when her family went into hiding, kept a diary of the experience until Aug. 4, 1944, when the inhabitants of the Secret Annex were arrested after someone betrayed them.
Frank died in a concentration camp of disease and exhaustion. A friend kept her diaries for safe keeping and after the war, Otto Frank, the only person of the eight to survive the concentration camps, read his daughter's diary and published it, garnering a worldwide response that has continued to this day.