The former oil tycoon arrived in Germany a free man Friday after more than 10 years behind bars, in a whirlwind release hours after his surprise pardon by President Vladimir Putin.
"We welcome the pardon and release from prison of Mikhail Khodorkovsky," Kerry said in a statement Friday.
"We have repeatedly expressed our concerns about due process violations and selective prosecution in Russia, including against Khodorkovsky and his business partner Platon Lebedev, who remains in prison."
Khodorkovsky, a former oil tycoon, was escorted out of his prison in northwestern Russia, in a hush-hush operation worked out behind the scenes with the German government and brokered by Berlin's former foreign minister Hans-Dietrich Genscher.
He then boarded a plane that landed at Berlin's Schoenefeld airport.
"The United States supports the rights of all Russians to exercise their freedoms of expression, association, assembly, and belief, regardless of their political views. These rights are enshrined in the Russian Constitution as well as in international agreements to which Russia has committed itself," Kerry said.
The release drew the curtain on the highest profile criminal case in post-Soviet Russia which has harmed the country's investment climate and become a symbol for the selective persecution of Kremlin foes under Putin.
"The United States strongly encourages Russia to pursue reforms that establish a transparent, independent, and reliable judicial system that upholds its commitments to human rights, the rule of law, and non-discrimination," Kerry said.
By accident or design, the release has coincided with a major amnesty for prisoners convicted of non-violent crimes that is expected to see the Pussy Riot punk rockers freed in the next days.
Thirty foreign and Russian Greenpeace activists, arrested on hooliganism charges after their protest against Arctic oil drilling, are also expected to escape prosecution.
Khodorkovsky had been due to be released in August 2014 but Russian prosecutors earlier this month raised the threat of a third trial for him on money-laundering charges.