The amount has been paid to Rajasthan Roadways by UP State Roadways Transport Corporation (UPSRTC).
The Congress government in Rajasthan had sent a bill of Rs 36.36 lakh for the buses for sending students from Kota last month.
Chief Minister Yogi Adityanath has sent buses to bring back students stranded in Kota during the lockdown and some extra buses had been arranged by the Rajasthan government.
About 12,000 students from UP, studying in Kota for engineering and medical entrance exams, were brought back to the state in the third week of April.
The UP government said it had sent 560 buses to ferry students but as the number of students was more than expected, it requested Rajasthan government to send the remaining students to Fatehpur Sikri and Jhansi on UP-Rajasthan border on their own buses.