Hollande had already visited in 2014 and remains the most prominent head of state to come to Iraq since the launch two and half years ago of a US-led coalition against the jihadists.
The French president, who is travelling with Defence Minister Jean-Yves Le Drian, will also stop in the autonomous northern region of Kurdistan during his one-day visit.
"Taking action against terrorism here in Iraq is also preventing acts of terrorism on our own soil," he said at a base of Iraq's elite Counter-Terrorism Service near Baghdad.
The jihadists then gained more territory in August 2014, forcing hundreds of thousands of people to flee from areas that had been controlled by the Kurdish peshmerga forces.
Since it joined the United States in the coalition in September 2014, French aircraft have conducted 5,700 sorties, around 1,000 strikes and destroyed more than 1,700 targets, according to defence ministry figures. France has 14 Rafale fighter jets that are stationed in Jordan and the United Arab Emirates and taking part in coalition operations.
Australia, Italy and Britain are also part of the 60- member coalition supporting Iraq's efforts against IS.
French nationals are also among the largest contingents of foreign fighters in IS and security agencies now fear the disintegration of the "caliphate" in Iraq and Syria will result in an influx of returning jihadists bent on carrying out terror attacks in their home countries.
Hollande is also expected to voice support for reconciliation and unity in Iraq, where observers fear an end to major operations against IS could see old internal divisions resurface.
Hollande was scheduled to hold talks with Prime Minister Haider al-Abadi, who hails from the main Shiite political bloc, President Fuad Masum, a Kurd, and parliament speaker Salim al-Juburi, one of the country's most prominent Sunni politicians.
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