The move, with an amnesty for the two jailed members of the Pussy Riot punk band and the 30-member crew of a Greenpeace ship, appears designed to placate international critics of Russia's rights record ahead of February's Winter Olympics in Sochi.
Mr Putin waited until just after his tightly choreographed annual news conference to make the announcement, dropping the biggest news of the day after journalists had peppered him with questions, including one about Khodorkovsky, for four hours.
Mr Putin said that Khodorkovsky, who is set to be released in August 2014, had submitted an appeal for pardon, something he had refused to do before.
Mr Putin said: "He's citing humanitarian aspects - his mother is ill. A decree to pardon him will be signed in the nearest time."
Critics have dismissed tax evasion and embezzlement charges against Khodorkovsky as a Kremlin vendetta for challenging Mr Putin's power.
In his press conference, Mr Putin also confirmed that an amnesty approved by the Kremlin-controlled parliament on Wednesday will apply to the two members of Pussy Riot still in jail and the Greenpeace crew facing hooliganism charges for their protest at a Russian oil rig in the Arctic.
Asked whether he felt sorry for the women, Mr Putin stood by his strong criticism of their irreverent protest at Moscow's main cathedral, describing it as a publicity stunt that "crossed all barriers".
He also alleged that the Greenpeace activists were trying to hurt Russia's economic interests. He added that he did not mind that charges against the Greenpeace team were dropped under the amnesty bill, but that he hoped that "this will not happen again".
Mr Putin weathered months of protests against his rule in 2011-2012, when 100,000 gathered to oppose his return to the presidency. A demonstration in May 2012, a day before his inauguration for a third term ended in scuffles with police.
The amnesty bill included only eight out of 26 people tried or awaiting trial in connection with that protest. Two were freed in a court as Mr Putin's conference went on.
Mr Putin defended the decision not to offer amnesty to others, saying that their release would give a bad example. "No one should be allowed to violently trample on the law," he said.
Amid a strain in Russia-US ties, he also offered surprising support to President Barack Obama by saying that US National Security Agency surveillance is necessary to fight terrorism. The government should "limit the appetite" of the agency with a clear set of ground rules, he said. Mr Putin, a 16-year KGB veteran and its former chief, said while the NSA programme "isn't a cause for joy, it's not a cause for repentance either".
Asked about former NSA contractor Edward Snowden, whom Russia has granted asylum, Mr Putin insisted that Moscow isn't controlling him and reaffirmed it made providing refuge to Mr Snow-den conditional on his halting what he called anti-American activities.
Mr Putin also dismissed a report that Moscow stationed missiles in the Kaliningrad region that borders Nato and EU members Poland and Lithuania, but said that he continues to consider such a move a possible way of countering the US-led missile defence system in Europe.