The case led to widespread shock in Kenya and around the world after police ordered some of the alleged attackers to cut grass as punishment.
On Monday, hundreds of people marched through the town of Busia to demand justice for the girl, known as "Liz".
She suffered a broken back and serious internal injuries.
The girl was attacked and repeatedly raped in June as she returned from her grandfather's funeral in Tingolo village in western Kenya's Busia County.
The BBC's Robert Kiptoo reports from outside court in Busia town that the trial is being held in-camera because the accused and alleged victim are minors.
He understands that the girl has already testified, and will now be cross-examined by the defence lawyer.
Her family has been barred from the courtroom, along with the family of the accused, our reporter says.
There are no protests outside the court, he adds.
More than 1.3 million people have signed an online petition demanding that the attackers are prosecuted.
Police say they are continuing investigations into the five other alleged attackers.
Her case caused an uproar after Kenya's influential Daily Nation newspaper reported that police in Busia had ordered three of the suspects she identified as her rapists to cut grass as punishment and had chosen not to prosecute them.
Police chief David Kimaiyo then intervened, and promised that a thorough investigation would take place.
Under Kenyan law, anyone convicted of gang rape face a sentence of between 15 years and life in prison.
One of the six teenagers accused of gang-raping a 16-year-old girl in Kenya and dumping her in a pit latrine has gone on trial.