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."
Hiddink would be a highly attractive prospect to any country needing a new coach going into the June 11-July 11 World Cup finals, should the Russians let him go early.
He took the Netherlands to the semi-finals in 1998 and matched that feat with co-hosts South Korea in 2002 before helping the unfancied Australian team to reach the knockout stage in 2006.
Hiddink has been linked with several national team coaching jobs in recent weeks, although there are likely to be plenty of top clubs among his suitors as well.
During his spell with Russia, Hiddink also managed Premier League Chelsea for a few months and helped them to win the FA Cup last season.
