Police said Biswajit Bhowmik, who had been absconding after the incident, was apprehended yesterday from Joalikhamar village of the same district and being interrogated by police.
Bhowmick allegedly raped his sister-in-law on Sunday night and was at large ever since.
The woman, admitted to Tripura Sundari hospital on Sunday, was taken to the Agartala Government Medical College next day, Police said.
The ruling CPI-M and opposition Congress both condemned the incident and called for exemplary punishment for him.