A spokesman said militants had gained ground inside Afghanistan and had to be stopped from extending their influence.
He said the "Khyber 4" operation, backed by the air force, would focus on the mountainous Rajgal Valley area in Khyber Agency.
Pakistan has previously denied the presence of IS on its territory.
However, the growth of the group - often referred to as Daesh - in neighbouring Afghanistan has alarmed Islamabad and the group has claimed several attacks in Pakistan over the past two years.
