The IMF said on Monday that the Greek government had paid about two billion euros (USD 2.2 billion) of its arrears.
"I can confirm that Greece today repaid the totality of its arrears to the IMF.... Greece is therefore no longer in arrears to the IMF," said the IMF spokesman Gerry Rice.
Rice added that the IMF was now "ready to continue assisting Greece in its efforts to return to financial stability and growth."
Greece failed to make payments to the IMF after it missed two deadlines on June 30 and July 13, amid negotiations with European leaders over its financial crisis.
Greece recently received a short-term loan of 7.16 billion euros (USD 7.77 billion) from the European Union (EU) in return for reforms, which made Monday’s repayment to the IMF possible.
Athens must also make a 4.2-billion-euro (USD 4.5 billion) payment to the European Central Bank (ECB).
The announcement by the IMF comes as Greek banks reopened after being closed for three weeks in a move aimed at avoiding the collapse of the country’s banking system.
Since 2010, Athens has received two bailout packages worth a total of 240 billion euros (USD 272 billion), from the international lenders - the European Commission, the IMF and the ECB - following the 2009 economic crisis, in exchange for imposing tough austerity measures.
Greece was at risk of having to leave the eurozone if it failed to reach a deal with European leaders over the debt crisis.
Despite widespread domestic opposition, the Greek government last week agreed to raise taxes, overhaul the pension system and carry out privatizations in order to receive a new bailout of 86 billion euros (USD 93.3 billion) over the next three years.
On July 17, Greek Prime Minister Alexis Tsipras reshuffled his cabinet and sacked 10 of members of his team, including Energy Minister Panagiotis Lafazanis, who had refused to back talks aimed at securing the new bailout deal.