One of the most respected coaches in world football, Hiddink had been in charge of Russia since 2006, taking them to the semi-finals at Euro 2008 but failing to successfully negotiate qualifying for this year's World Cup finals in South Africa.
"After a very comfortable conversation with the new chairman of the Russian association we decided to break up on June 30," Hiddink, 63, said in his column.
"We made the decision right now so the Russian association has enough time to find my successor."
The Russian FA (RFU) confirmed Hiddink's decision to quit.
"Guus Hiddink has informed RFU president Sergi Fursenko that he will resign as Russia coach at the end of his contract," the FA said in a statement on its website.
"Guus himself had made such a difficult decision and we respect his choice."
