This is first time Mr president will be absent at the mosque since he returned to the country after a 49-day medical vacation in the UK.
However, some of the dignitaries who usually join him at the mosque were there for prayers.
Among them were Abdullahi Ganduje, governor of Kano, Ibikunle Amosun, his Ogun counterpart, and Abdulaziz Yari of Zamfara.
The absence of the president in public functions has been a source of concern.
On Wednesday, Buhari missed the federal executive council meeting for the second time in a row, fuelling reports about his health condition.