Punnaram Cholli Cholli is the story of Biju (Rahman) a motherless boy from a rich family. He studies in Ooty in a boarding school and spends his vacations in his father's ancestral village. His father, a busy lawyer has no time for him or his vast property. The property is looked after by Bharat Gopi and his assistant, Nedumudi Venu. The duo live off the property selling the produce on the sly because Biju is too innocent to notice anything. Zarina Wahab, the niece of the local baker (Innocent) reaches the village to join for duty at the local bank. Biju saves her from reaching her uncles house via a long route suggested by Nedumudu Venu and Bharat Gopi. The two become friends. Zarina considers Biju her younger brother and the lonely Biju becomes good friends with her. The conniving duo, Nedumudi Venua and Bharat Gopi, mislead Rahman into believing that Zarina is in love with him and desires him as her husband. They want the boy out of their way so that they can pilfer from the farm without having to look-out for him. The innocent boy falls for their story. This leads to misunderstandings, disappointment, jealousy and the duo further goad him to take revenge for a perceived rejection which leads to a terrible tragedy.