Ghani secured 81 votes as he contested for the slot against Laiq Muhammad Khan of Awami National Party (ANP).
Pakistan Tehreek-e-Insaf (PTI) had nominated Mushtaq Ahmad Ghani for speaker and Mehmood Jan for the slot of deputy speaker.
Jamshed Mohmand of PML-N was nominated as deputy speaker by the joint opposition.
Meanwhile, voting is under way for speaker and deputy speaker of the Sindh and Balochistan assemblies.
A secret ballot is also being held for National Assembly speaker and deputy speaker.
Pakistan Tehreek-e-Insaf (PTI) – the majority party in the House – has nominated Asad Qaiser for the slot of NA speaker, while the joint opposition has fielded Syed Khursheed Shah for the post.
For deputy speaker, PTI has named Qasim Suri while the joint opposition has nominated Muttahida Majlis-e-Amal leader Asad Mahmood.