Now, she is at the center of a growing campaign which is demanding a better environment for her to live out her final days.
"I was shocked and dismayed to see the conditions of her confinement firsthand," wrote Canadian animal rights activist Ulara Nakagawa in a blog post after she visited the zoo in October.
"Totally alone in a small, barren, cement enclosure, with absolutely no comfort or stimulation provided, she just stood there almost lifeless, like a figurine."
The blog post, which included a lonely picture of Hanako, spread quickly on social media and sparked an online petition to and crowdfunding campaign on Indigogo. The petition now has nearly 420,000 signatures, and nearly $30,000 has been raised.
Plan to improve her life
The "Help Hanako" campaign proposes that the elderly elephant be moved to a sanctuary in Thailand, or have her current surroundings drastically improved.
As Hanako chomps on a banana on a sunny day in Tokyo, she appears oblivious to the storm of controversy she has created.
And the zoo manager also seems a little bemused.
"I was surprised. Those who signed the petition didn't know much about (Hanako)," Hidemasa Hori, Deputy Director and General Curator at Inokashira Park Zoo, tells CNN.
"They would understand that the present situation is the only solution after they actually meet her and learn how she has been taken care of."
A life in Tokyo
At 69, Hanako has already far exceeded the usual 40-year life expectancy of captive elephants. She arrived in Japan when she was two years old, as a gift from the Thai government after World War II.
"She has only one tooth left, so she cannot eat without special care," Hidemasa
Hori says. "We feed her special fruits and Japanese-style wheat rice ball. Since banana skins are too hard for her to eat, we peel off the skin for her."
Hori insists that her solo confinement is necessary for safety reasons, as she is a "difficult and sensitive elephant" who has trampled two people to death in her enclosure in the past.
Deadly past
"She is, so to speak, a killer elephant," Hori says. "The first accident was when a drunk man sneaked into her enclosure and died. The second incident involved a caretaker. Even after that, there were a few close calls."
Hori says Hanako's temperament and advanced age mean that any move would be too traumatic.
"She is difficult old lady, who overreacts to small changes of circumstance," Hori says. "We don't want to take such risks. We think it would be better for her to spend the rest of her life here under familiar conditions, being loved by the visitors and well taken care of by the handlers."
But Ulara Nakagawa insists that more can be done to make Hanako's final days more pleasant.
Using the funds raised in the online campaign, Nakagawa and an American elephant expert, Carol Buckley, flew to Tokyo this week to meet with the zoo managers to discuss Hanako's future.
"Hanako's zoo has agreed to meet with me," Nakagawa says in a YouTube video about the campaign. "Carol and I will meet with the zoo to discuss in an open and collaborative way what is best for Hanako."
Easier said than done
Animal welfare experts say the options are limited.
"Japan has no sanctuary facilities for elephants," the Born Free Foundation said in a statement. "The first step to assist Hanako would be to conduct a proper health and welfare evaluation, to determine whether she is a candidate for travel of any kind and, if not, how to mitigate the multitude of issues she faces at Inokashira Zoo."
Nakagawa agrees this is the best course of action.
"If this move is dangerous for her in any way, we would want to make immediate and significant improvements to her current enclosure," Ulara Nakagawa says.
The regular visitors of the park hope she can stay.
"I understand people want to give her good surroundings to live the rest of her life," says Kaori Igari, a mother with two children who often visits Hanako. "But I personally want her to stay here, she is a symbol of Inokashira Park Zoo. I would feel sad if we lost her."
"Visiting Hanako is the one of purpose of my life. I'm old, and Hana-chan is old too, I share the time with her," says Nobuko Iima, who visits Hanako every week. "I don't think she is unhappy living here. I would like her to live out her life being loved by the people here."