The US defence secretary reiterated his commitment to assisting the autonomous northern Iraqi region, which has been at the forefront of efforts to counter the jihadists.
Carter "commended President Barzani on the battlefield successes they've achieved on the ground in coordination with US and coalition air power," a Pentagon statement said.
Several high-ranking Kurdish military officials attended the talks in the Kurdish capital Arbil with Carter, on his first trip to Iraq since taking office earlier this year.
An international coalition has since developed and carried out thousands of air strikes, many in support of Kurdish peshmerga forces fighting IS on the ground.
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More than 1,200 Kurdish peshmerga fighters have been killed in fighting with IS, which last year swept into several areas controlled by the Kurds, who are now trying to take them back.
Many of the 3,500 US advisers and trainers that have been deployed to Iraq in the past year are stationed in Kurdistan.
He was in Baghdad on Thursday and met several Iraqi officials, including Prime Minister Haider al-Abadi and his counterpart Khaled al-Obeidi.
Relations are strained between the federal government in Baghdad and the autonomous administration in Kurdistan.
Barzani, whose forces have de facto seized several oil-rich, contested areas on the back of last year's IS offensive, has threatened to organise a referendum on independence.
Carter stressed during his meeting with the veteran Kurdish leader that Washington's assistance to Kurdistan as part of the war against IS would not bypass Baghdad.
Carter's visit came as Iraqi forces were upping the pressure on IS in its stronghold of Anbar, a vast Sunni province which stretches from the outskirts of Baghdad to the borders with Syria, Jordan and Saudi Arabia.