The fire broke out in the house but there was no report of any casualty, police said adding that the cause of the fire was not known but they were investigating the matter.
The girl who was a student of class XI went missing on October 25, 2013 while returning from private tuition. Her body was found on October 28.
Her family had alleged that she was gangraped and murdered.
The CID took over the case and arrested the accused.
The girl's family members alleged that their house was set on fire by the accused to frighten people from deposing in the court against the accused.