The Hungary international was stretchered off the field during the Latics' goalless draw with Barnsley at the weekend with anterior cruciate ligament damage.
Bogdan, who was due to remain at the DW Stadium until next summer, is now facing a nine-month spell on the sidelines and has therefore returned to his parent club to begin his road to recovery.
"I have just received the result of my MRI scan, which showed that I tore my ACL in my right knee," he is quoted as saying by the Liverpool Echo. "It will be a lengthy recovery. I am sure I will return stronger."
Bogdan had started all 17 of Wigan's Championship fixtures prior to being withdrawn on the hour against Barnsley.