The 12-member team left aboard a Bangladesh Biman flight around 12:45pm on Monday, said airport Armed Police Battalion Inspector Iqbal Hossain.
Khan will sit with the Myanmar government to discuss the Rohingya crisis, which has seen over half a million members of the minority cross the border into Bangladesh since the start of a military crackdown on Aug 25.
Another 400,000 Rohingyas had taking refuge in Bangladesh for the past few decades, prior to the recent influx.
Accompanying the home minister will be two secretaries of the his ministry, the inspector general of police, the director general of the coast guard, the director general of the drug regulation agency and other top ministry officials.
The home minister will also sign two agreements on border security with Myanmar, according to Home Ministry Public Relations Officer Sharif Mahmud Apu.
The home minister has said he will discuss the repatriation of Rohingyas at the meeting.