The International Security Assistance Force commander will call on Pakistan Army chief Gen Ashfaq Parvez Kayani, the military said in a statement.
The interaction will focus on reviewing progress made in implementing "recently evolved border coordination measures and standing operation procedures", the statement said without giving details.
This will be Allen's second visit to Pakistan this month after relations between Islamabad and Washington improved following months of tension.
He visited Islamabad earlier this month for talks on security along the Pakistan-Afghanistan border.
High level contacts between the two sides resumed after Pakistan reopened NATO supply lines to Afghanistan in July after a seven-month blockade.
The routes were closed last November after 24 Pakistani soldiers were killed in a cross-border NATO air strike.
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Ahead of his visit, Allen said Afghan Taliban chief Mullah Muhammad Omar was hiding in Pakistan and sending fighters to Afghanistan.
"Omar lives in Pakistan, as do many of his commanders," Allen wrote in an article in The Washington Post.
On the other hand, the Pakistani military has accused foreign and Afghan forces of not doing enough to stop cross-border raids by Pakistani Taliban fighters based in the Afghan provinces of Kunar and Nuristan.
The Taliban militants sneaked into Afghanistan to escape operations launched by the Pakistan Army.