The incident had taken place on Saturday.
The accused, identified as Anna a.k.a Shubham Modwal, is a resident of Kotwali area. He was also the caretaker of the facility.
The police had registered a case under Section 376 of IPC against the prime accused who was absconding soon after the incident.
Circle Officer (Pratapgarh City) Abhay Pandey told reporters that a joint team of Kotwali police and the crime branch arrested the prime accused near Bhupiamau crossing.
The accused was wanted by police in connection with a case registered against him under section 376 of IPC.
The woman, who lodged the FIR, claimed that she had reached Pratapgarh railway station with her husband on Friday night as they had to board a train for Ahmedabad.
At around 4 a m on Saturday, when her husband went to bring tea and breakfast, she went to the public toilet where she was raped.
The woman and her husband approached the Kotwali police soon after to lodge a complaint and she was sent for medical examination.