The premier flew to the base in northern Punjab state to conduct an aerial survey of the area near the Pakistan border, following the strike by gunmen whom Indian officials suspect belonged to a banned Pakistan-based group.
It follows criticism from the opposition Congress party of the apparent security lapse that allowed the militants to infiltrate the strategically important base.
Security forces on Friday said they had finally sanitised the sprawling installation after a lengthy search operation, PTI said.
Modi called on Pakistan earlier in the week to take action against those behind the attack and said rime Minister Nawaz Sharif had given assurances that his government would take “prompt and decisive action”.
The attack on Pathankot came just days after a landmark visit to Pakistan by the Indian premier raised hopes of improved relations.