Jarnail Singh will arrive here on Friday to take up the job.
A division bench of Justices N. Koteswor and Kh. Nobin passed the order in a packed courtroom in response to a PIL.
The order asked all concerned to extend cooperation to the Administrator and warned that anyone violating the direction would invite contempt of court proceedings.
Because of the ongoing impasse, the students were suffering, the court observed.
Trouble started earlier this year when teachers, students and staff of Manipur University demanded the removal of Vice Chancellor A.P. Pandey on charges of administrative and financial irregularities.
It led to the closure of the university for 85 days.
The university community has now been demanding the removal of Prof K. Yugindro, the latest Vice-Chancellor.
(With inputs from agencies.)