In a speech in Cairo on Monday, Rice praised the desert kingdom's "brave citizens" who were "demanding accountable government" before flying to Riyadh.
While acknowledging that some first steps towards more openness had been taken, in a reference to recent municipal elections, she said: "Many people still pay an unfair price for exercising their basic rights."
"Three individuals in particular are currently imprisoned for peacefully petitioning their government - and this should not be a crime in any country."
In May, activist Ali al-Demaini was sentenced to nine years in prison, Abd Allah al-Hamed to seven years and Matruk al-Faleh to six years, according to Hamed's brother Issa.
The trio was among a dozen activists arrested in the kingdom in March 2004 on charges of demanding a constitutional monarchy. The others were released after pledging to no longer lobby publicly on the issue.
They were accused of using Western terminology in formulating their demands. They also allegedly questioned the king's role as head of the judiciary.
Rice is due to meet Saudi Arabia's Crown Prince Abd Allah bin Abd al-Aziz and Foreign Minister Prince Saud al-Faisal during her stay, the latest leg of a tour that has already taken her to Israel and the Palestinian territories, Jordan and Egypt.