Mrs Clinton said: "I am pleased that we were able to facilitate Chen Guangcheng's stay and departure from the US embassy in a way that reflected his choices and our values.
"Mr Chen has a number of understandings with the Chinese government about his future, including the opportunity to pursue higher education in a safe environment," she said.
"Making these commitments a reality is the next crucial task. The United States government and the American people are committed to remaining engaged with Mr Chen and his family in the days, weeks, and years ahead."
After leaving the US embassy, the Chinese dissident had a telephone call with Mrs Clinton in which he reportedly said: "I want to kiss you."
Mr Chen's lawyer Li Jinsong said he had spoken to his client on the phone. He said Mr Chen was "very happy and wants to hug all his friends".
Mr Li said the dissident had told him he now had "true freedom", his rights were now protected by the national law and he was "a free citizen".'Threats' to family
However, a close friend of Mr Chen told Associated Press that the dissident had chosen not to go to the US because he had been warned his wife would face recriminations if he did so.
Zeng Jinyan, herself an activist in Beijing, told the BBC she had spoken to Mr Chen and learned he had opted to stay in China to protect his family.
Ms Zeng said that Mr Chen "had no choice" because "thugs with sticks" were waiting for him and his family in their home village in Shandong province.
She said: "It's impossible, he couldn't do anything. He said, 'please help me'."
Bob Fu, of Texas-based rights advocacy group ChinaAid, said reliable sources had also told it that Mr Chen had left the embassy because serious threats to his immediate family members were made by the Chinese government.
"We are deeply concerned about this sad development if the report about Chen's involuntary departure is true," Mr Fu said.
These reports contradicted one US official, who said Mr Chen had "made clear from the beginning that he wanted to remain in China, and that he wanted his stay in the United States Embassy to be temporary".
The official, who wanted to remain anonymous, said the dissident had gone into the embassy on 26 April "requesting medical treatment from the embassy" - which had been given.
The official said China had "acknowledged that Mr Chen will be treated humanely while he remains in China.
"He has been reunited with his family - his wife and two children - at the hospital, and they remain together with him as a family. He had not seen his son in a few years, and his wife had not seen [the son] either, so this was a family reunification after a long and difficult separation."
Mrs Clinton said she was glad to have the chance to speak to Mr Chen and "to congratulate him on being reunited with his wife and children".
Chinese foreign ministry spokesman Liu Weimin earlier said Mr Chen had been taken into the US embassy "via abnormal measures", the Chinese authorities were "strongly dissatisfied", and the US should apologise.
Mr Chen, who has been blind since childhood, has long been a high-profile figure and international rights groups have frequently expressed alarm at the treatment of him and his family.
He was placed under house arrest in 2010 after spending more than four years in jail for disrupting traffic and damaging property.
Mr Chen exposed how local authorities in Linyi, in Shandong, forced thousands of women to have abortions or be sterilised as part of China's one-child policy.
Mr Chen's colleagues said the escape from house arrest had taken months to plan, and was carried out with the help of a network of friends and activists.
He scaled the wall that the authorities had built around his house, and was driven hundreds of miles to Beijing, where activists say he stayed in safe houses before fleeing to the embassy.
Several people involved in Mr Chen's escape have been detained or have disappeared in recent days.
Yes, you read that right, several people have disappeared in recent days because of helping Chen escape. You really think he is alright? Hillary just didn't want this guy interfering with her visit to China so she made sure he was no longer an issue. If there were threats to his family, the right thing to do was to pressure the Chinese government until they let his family go as well, not surrender to a bunch of Communist thugs. Last time, the Obama administration betrayed a dissident in order to help a major Obama donor (Jeffrey Katzenberg), I wonder if there was another one involved here?