He was responsible for some of the most popular superhero characters in history including Spider-Man, X Men, the Incredible Hulk and Iron Man.
Lee's daughter, J.C. Lee, confirmed his death to Reuters news agency, saying that her father "loved his life and loved what he did for a living".
She added: "His family loved him and his fans loved him. He was irreplaceable."
Tributes to Lee have poured in from the world of film including messages from actors who starred in Marvel movies.
"There will never be another Stan Lee," tweeted the actor Chris Evans, who played Captain America on the big screen.
"For decades he provided both young and old with adventure, escape, comfort, confidence, inspiration, strength, friendship and joy."
Wolverine actor Hugh Jackman said the world had "lost a creative genius".
Iron Man star Robert Downey Jr posted a photo on Instagram of himself with Lee and an image of a love heart.
"I owe it to you all," he wrote.
"Rest in Peace Stan."
Meanwhile, Josh Brolin - who played villain Thanos in Avengers: Infinity War - said: "To those of us who have been so deeply affected by the humanity of his imagination, the understanding of reaching beyond our potential and the necessity of tapping into our immeasurable imaginations, we thank you."
Lee, a writer and editor, worked with artists such as Jack Kirby and Steve Ditko to turn Marvel into a major comic book brand in the 1960s.
His characters, while imbued with incredible abilities, were allowed to have flaws and complexity: they worried about love and money and would sometimes feel insecure.
Lee told NPR News in 2010 that his characters were "human as well as super", and that he wanted to "learn a little about their private lives".
In recent years Lee had become known for his cameos in Marvel films. He pulled a girl away from falling debris in 2002's Spider-Man and was a casino customer in this year's Black Panther.
In Spider-Man 3 he played "Man in Times Square", and said: "You know, I guess one person can make a difference... enough said."
Lee was born Stanley Martin Lieber in New York in December 1922, the son of Jewish immigrants from Romania.
When he was 17 he became an errand boy at Timely Comics - which evolved in Marvel - and soon began to write.
Initially, as well as tales of superheros, he wrote westerns and romances.