Turkey's President Erdogan axes friendly university chief
The report gave no official reason for Bulu's removal, however CNN Turk reported that the move follows a conversation had on Wednesday by the Council of Higher Education concerning his behaviour and words during the previous half a year.
Erdogan had described protesters against Bulu as "terrorists who wanted to raid the university rector's office", promising to take "whatever [action] is necessary".
Bulu had previously stood for election to parliament under the banner of Erdogan's AK Party.
A new rector, Mehmet Naci Inci, will take over the reins on an "acting" basis, according to the Turkey's Sabah news outlet, which is aligned with the country's authorities.
Inci previously led the physics department and was made deputy university chief while Bulu was in office.
Former and current pupils as well as members of staff rallied in opposition to Bulu since he was put in place at the beginning of the year, arguing that the job holder should be elected.
Turkish authorities have detained protesters and raided the homes of demonstrators.
While Bulu's time as head of Bogazici University has now ended, it was a chance for the authorities to hold more sway over appointments at the institution.
The educational establishment used to be a US institution and is considered as too friendly to the West by many who side with the Turkish president.