Balawing, who just turned 18, is 23.5 inches (59.9 cm) tall, succeeding previous title holder Khagendra Thapa Magar from Nepal, who is 26 inches (67.08 cm) tall.
A team from Guinness World Records made the announcement in the remote town of Sindangan, where Balawing lives, on his 18th birthday on Sunday. Claimants for the title must be at least 18 years old.
"We are happy on this day. We are proud of Junrey," his mother Concepcion said.
The Guinness team, led by Guinness World Records editor-in-chief Craig Glenday, measured Balawing both vertically and horizontally before declaring him the world's shortest man and handing him a certificate.
Balawing's father said his son, the oldest of four children, stopped growing in his first year. His speech is also stunted and his conversations are limited to short phrases.
Balawing mostly stays at home, needing assistance to move around. His condition has prevented him from attending school.
While the award does not come with a cash prize, Glenday said the team hopes that publicising Balawing's case will draw the attention of medical experts who may be able to help him. Local medical practitioners have not been able to explain his growth disorder.
"The previous record holder had been given medical care... He even had free surgery provided by the U.S.A. So there are benefits to being a record holder," Glenday said.
"We feel for him because of his size. Obviously, being that size, it's quite a compromised life. We hope that by publicising his case, medical practitioners will pay attention."
A smiling Balawing celebrated his 18th birthday with balloons and a cake.
