The 16-year-old was allegedly dumped in a sewage ditch after the attack, local human rights groups said.
She later identified three of six suspects, who cut grass at a police station and were freed afterward, according to the groups.
Protesters made their way through downtown to the police chief's office to deliver a global petition demanding the arrest of the suspects. They chanted "justice for Liz" and carried placards with the same words.
Men and women waved underwear, and stuck other underwear on the gates of the police chief's office.
Some danced, beat drums and cried.
Liz is the nickname given to the teen by the local media. CNN does not identify alleged victims of sexual abuse.
Cries for help
Liz was walking home from her grandfather's funeral in the northwestern town of Busia when the alleged attack occurred.
Hours later, neighbors heard her cries for help and pulled her out of a latrine, bloody with broken bones, rights groups said.
She identified three of her alleged attackers, and an angry mob of neighbors hauled the suspects to the local police station.
But what followed added to the outrage.
Police ordered the suspects to cut grass in the yard, then released them shortly after, said Milanoi Koiyiet, a representative for Kenya's Coalition on Violence Against Women, which is providing the teen with free legal help.
Outcry grows after rape suspects are ordered to cut grass as punishment
The suspects' whereabouts are unknown after they left the police station. But a top aide for the Kenyan police chief said an investigation is under way.
"We are going to make sure that her case is attended to with the seriousness that is deserved and that we are making all efforts to make sure that the culprits are arrested wherever they are," said William Thwere, chief of staff for Kenya police.
Reports that the suspects have crossed the border to neighboring Uganda will not hamper the investigation, he said.
"We have put mechanisms in place to make sure that they are located even across the border where it is being alleged that they are," Thwere said.
She has to use a wheelchair
Word of the attack got out in October -- three months later --- when one of her doctors, outraged by the incident, called a journalist at the Daily Nation newspaper. The newspaper broke the story and is spearheading a fundraiser to pay for her medical bills.
By then, Liz had been hospitalized several times and had to use a wheelchair. She also suffered from a condition that makes her unable to control her bowels as a result of the rape, the Coalition on Violence Against Women said in a statement.
She's been in and out of the hospital since June. Her mother, a small-scale farmer, leased her land to make extra money to send her to a bigger hospital in the nearby major city of Kakamega, according to Koiyiet.
Outrage on social media
There has been an outcry on social media, with Kenyans demanding the arrest of the suspects and the officers who ordered them to cut grass. The six suspects are between the ages of 16 and 20, Koiyiet said.
Global campaigning network Avaaz launched an online petition demanding justice. It had more than 1.3 million signatures by the time protesters delivered it to the police chief's office Thursday.
More protests planned
Local rights groups have teamed up to demand justice in the case and are planning more protests until arrests are made.
At least 32% of Kenyan girls younger than 18 experience some form of sexual violence, according to a report released last year by the government and the United Nations.
The numbers may be higher because many rapes go unreported for fear of stigma.
If found guilty of gang defilement, the suspects face 15 years to life in prison, Koiyiet said.