Nancy Sinatra Junior, Frank and Nancy Senior's daughter, tweeted on Friday that her mother died at 6:02 pm.
"Nancy was giving herself a manicure on the front porch when Frank came over with his ukulele and began to serenade her", according to an account on Sinatra's website.
Nancy, for the most part, avoided the spotlight and chose to instead dedicate her life to her children.
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He left his wife for Ava Gardner in the early 1950s.
Frank and Nancy, whose maiden name was Barbato, started dating as teenagers; they married in 11939 at a church in New Jersey. The family have confirmed Nancy Sinatra has died aged 101.
The marriage came just as Frank Sinatra's singing career was starting to take off. "Godspeed, Momma. Thank you for everything", she wrote.
In 1944, after Frank had become a pop music star, the family moved to Toluca Lake, Calif. from their Jersey City home, and had a third child, Tina, on June 20, 1948. Frank frequently requested food from her, foods she was known for being an expert at preparing, including Italian dishes. "She would never show it in front of us, never, but my room was next to hers and I would tiptoe out and I'd listen at the door and she'd be crying".
In 1966, journalist Gay Talese wrote of the couple: "There is no bitterness, only great respect and affection between Sinatra and his first wife and he has always been welcome in her home and has even been known to wander in at odd hours, stoke the fire, lie on the sofa, and fall asleep".