He remained at the Paris Observatory, which Napoleon II had renamed the Imperial Observatory. Arago requested that the Academy of Sciences replace him as Secretary, not because of the problems with Napoleon III, but rather because he felt that his health was failing, in particular his eyesight was by now very weak, and he could not properly carry out his duties.
Siya ay nanatili sa Paris obserbatoryo, na kung saan Napoleon II had muli ang Imperial obserbatoryo. Arago hiniling na ang Academy of Sciences palitan siya bilang Kalihim, hindi dahil sa mga problema sa Napoleon III, kundi dahil siya nadama na ang kanyang kalusugan ay nanghihina, partikular na sa kanyang paningin ay na sa ngayon masyadong mahina, at siya ay hindi maayos na isagawa ang kanyang tungkulin.