Ms Rice dropped in on Kurdish regional president Massud Barzani in Arbil, his northern capital, after an unannounced visit to the Iraqi capital Baghdad.
"The Kurdish people will ... certainly be better served if Baghdad and its surrounding areas are stable and democratic," Ms Rice told reporters at a joint press conference with Mr Barzani.
Grateful for US support in ousting former Iraqi dictator Saddam Hussein, Iraq's Kurds have put their long-cherished dreams of independence on hold while the Baghdad government struggles to rebuild the war torn country.
Washington fears a Kurdish declaration of independence would accelerate the possible disintegration of Iraq and knows it would be bound to anger regional ally Turkey, which has a restive Kurdish minority of its own.
Kurdish leaders regularly warn that they will secede if the rights of their region - a union of three Iraqi provinces which has been broadly autonomous since 1991 - are trampled on by the Arab-led Baghdad administration.
Kurd murdered
Officials in Baghdad confirmed that a Kurdish member of Iraq's national parliament had been kidnapped and murdered during Ms Rice's visit, which came after Monday's breakthrough pledge by Iraq's political factions to work together to halt the bloodshed.
Ms Rice met Iraqi Prime Minister Nuri al-Maliki, President Jalal Talabani and senior leaders from both sides of Iraq's bitter sectarian divide between Sunni and Shi'ite factions.
The violence in Baghdad was in full evidence for Ms Rice's visit, with 16 US soldiers killed since Monday.
A rocket attack on the airport upon her arrival forced her military C-130 transport to circle the airfield for 45 minutes.
Ms Rice left Arbil after a delay of more than two hours because of aircraft problems and headed to London for a meeting of six major powers on whether to urge the United Nations to slap sanctions on Iran over its suspect nuclear program.