US leads a 60-nation coalition that has provided key support in the form of thousands of air strikes.
"We want to see an isolation operation begin around Raqa as soon as possible," Carter said during a visit to Iraq's autonomous region of Kurdistan to review an ongoing offensive to retake Mosul from IS.
"We are working with our partners there (in Syria) to do that," the US secretary of defence said, adding: "There will be some simultaneity to these two operations."
Iraqi forces launched a huge operation last week to retake Mosul, the last major city in Iraq under IS control.
The United States leads a 60-nation coalition that has provided key support in the form of thousands of air strikes, training to Iraqi forces and advisers on the ground.
The loss of Mosul would leave Raqa -- the de facto capital of the jihadists' self-declared "caliphate" -- the only major city still under IS control.
Carter said the idea of simultaneous operations against Mosul and Raqa "has been part of our planning for quite a while".
In Iraq, the coalition is allied with both federal forces and Kurdish peshmerga fighters in the Mosul battle.
But in Syria, the issue of which ground forces would be involved in an operation to retake Raqa would be far more complicated.
The United States has given support to Syrian rebels and the Kurdish-led Syrian Democratic Forces who have battled IS. But President Bashar al-Assad's forces, backed by Russia and Iran, are also fighting the jihadists.