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The arrest came two days after the girl allegedly died by suicide.
An officer of Vazhakkad police station said prior to her death, the 17-year-old girl had told her parents about what the karate instructor had done, but no complaint was lodged as per her wishes.
The girl had gone missing on February 19 evening and the same night her body was found in the nearby river.
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A case under the Protection of Children from Sexual Offences (POCSO) Act has been registered against the accused who was arrested on February 21.
Police also said that an investigation is underway into the circumstances that led to the girl’s death.
The karate instructor was an accused in another POCSO case in the past, but was acquitted in that, it added.