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.
"This operation was necessary because Daesh is getting established there and we have to stop the influence spreading into Pakistani territory through the Rajgal Valley," military spokesman Lt Gen Asif Ghafoor said.
IS in the region is mostly made up of former members of the Afghan and Pakistani Taliban and Gen Ghafoor reiterated the government's stance that the group has no established presence inside Pakistan.
"There is no organised infrastructure and we shall not allow them to establish themselves," he said.
"As regards inside Afghanistan, yes, Daesh is getting stronger there, is gaining strength. But still, we feel that it is not purely the Daesh which is there in the Middle East."
Photo by: Getty Images (The volatile tribal areas along the Afghan border have often posed security problems for Pakistan)