He then studied at the Imperial Medicine College (Ottoman Turkish: Mekteb-i Tıbbiye-i Şâhâne) graduating with distinction in 1885.

[7] He served briefly as military physician at the Greek border, before he had to return to Istanbul after catching typhus.

Besim Ömer was then sent to Paris, France, where he worked as an assistant physician at the Hôpital de la Charité, and completed his medical specialization in 1891.

He tried several times to open up a birthing center, his application was however declined by Sultan Abdul Hamid II (reigned 1876–1909).

In 1892, he established, secretly from the Sultan's Court, the country's first birthing clinic in a small building next to the Medical College.

[7] Besim Ömer countered the local mentality that prevented Muslim women from having jobs and touching men even for medical purposes.

In 1911, he personally trained daughters of well-known Muslim families in Istanbul in a six-month-long volunteer nursing course.

Besim Ömer led the way for Turkish women to become first female physicians by enabling a group of girls to enroll at the Imperial Medical College in 1922.