The Charity Commission said the money came from a company associated with Khordokovsky, who has been held in custody in Russia since last year for alleged fraud and tax evasion.
The Khordokovsky Foundation plans to fund up to 3,000 students and educational bodies in the Russian Federation from the income generated by the endowment.
"The commission, as usual in such cases, has worked closely with other regulatory agencies to ensure the foundation meets all legal requirements," said the commission in a statement.
The chair of trustees is Anthony Smith, president of Magdalen College, Oxford, and trustees include former Russian deputy prime minister Boris Saltykov.
Smith said: "The money has been in the UK for a long time. The foundation was set up some months ago, but we have not been operating because we were waiting for the legal registration of the charity.
"We will have a meeting of trustees in the next week or two, to decide on an investment programme and to build an advisory group on how we should be spending the money in Russia. We want to take the decisions slowly and carefully to be of most help to students of Russian origin."
Russia announced last weekend that it was moving ahead with plans to break up oil giant Yukos, in which Khordokovsky's Group Menatep is the core shareholder. The authorities also hit Yukos with a new tax demand of £3bn for 2003 on top of the existing bill of £13bn.
A spokeswoman for the commission said it did not take a view on Khordokovsky's tax affairs. "As a regulator our main concern is whether the purposes of the charity conform to the 1993 Charities Act, and to make appropriate checks. It does not extend to why and when a charity is formed."