Bogdanov will run as an independent candidate, as his party failed to make it into parliament at the December 2 polls, gaining only 0.1% of the vote. He had to produce at least 2 million signatures in support of his application, along with documents including proof of income and property.
He reportedly encountered certain problems with election officials, but the number of signatures deemed to be 'fake' was less than 5%.
Under Russian law, a candidate can be denied registration if more than 5% of the signatures are found to be invalid or false. Critics have called the requirement to raise 2 million signatures unrealistic and undemocratic.
Earlier on Thursday, the Central Election Commission (CEC) denied ex-premier and opposition candidate Mikhail Kasyanov registration, saying more than 13% of provided signatures proved to be fraudulent.
Kasyanov's press secretary said he would contest the CEC's findings, and his support team rejected the forgery claims as "political pressure."
Kasyanov is heavily associated with the gloomy Yeltsin era in Russia, and was himself involved in a series of bribery scandals during his premiership. He has little popular support in the country.
Bogdanov, 37, is known as a fierce advocate of Russia's integration into Europe.
"Russia is a European country, and Russians are Europeans. We must return to the European family," he said earlier in an interview. "We left it in 1917 [after the Bolshevik revolution] and we believe we must get back there by 2017."
He said his party had concrete programs to bring Russia closer to Europe and planned to raise the question of Russia's EU membership at a national referendum in 2009.
Bogdanov is the fourth officially registered presidential candidate after the ultranationalist LDPR leader Vladimir Zhirinovsky, Communist leader Gennady Zyuganov, and the ruling United Russia party's nominee Dmitry Medvedev.
Opinion polls put Medvedev - a first deputy prime minister openly backed as his successor by the popular President Vladimir Putin - in the lead among presidential hopefuls with almost 80% of electorate support.
