His return comes after an invitation of fellow co-founder Jack Dorsey, who was brought back as chief executive in 2015.
Mr Dorsey has been trying to reboot Twitter, which claims more than 300 million monthly users, but has struggled to turn a profit.
Twitter's stock bounced nearly 2% on the news.
Mr Stone said he will focus on the culture of the company.
"I'll shape the experience internally so it's also felt outside the company," he wrote. "More soon."
Mr Stone left Twitter in 2011, after the exit of fellow co-founders.
He went on to start the publishing platform Medium and a search app, Jelly Industries, which Pinterest acquired this year.
Twitter co-founder talks about the future of social media
Dorsey: Twitter will take time to fix
After a recent visit to Twitter, Mr Stone said he couldn't turn down the chance to work there again.
"When I stood next to Jack addressing the crowd of employees, I felt the energy, and I was overcome with emotion," he wrote in a post on Medium. "I realised in that moment that Twitter was the most important work of my life."
Mr Dorsey also shared the news on Twitter, writing: "Excited to have Biz's energy and heart back at Twitter! #BizIsBack"

The infant, still with her umbilical cord attached, was found in a black bag by a member of the public in Marston, Oxford, on 29 February.
The baby was discovered with no signs of injury and a coroner recorded that she was stillborn.
Police said they wanted to find out if her family had any religious beliefs.
Det Con Sarah Danzelman, from Thames Valley Police, issued a direct appeal to the baby's mother to get in contact with her.
She said: "Shortly we will be arranging for a funeral for your little girl and we want to make sure she is laid to rest in an appropriate way in line with any beliefs you have.
"We are very keen to give your baby a name - a name that means something to you. Please let us know what her name is."
She added that the funeral service, which has not been given a date yet, would be open to anyone who wished to pay their respects.
Twitter co-founder Biz Stone has said he plans to rejoin the social media site in the next few weeks.
[NEXT_CONCEPT]
Police have appealed to the mother of a baby girl found dead on a footpath to tell them the child's name ahead of her funeral.