More than 90 people died in clashes during the 2010 protests.
Abhisit Vejjajiva, who leads the opposition Democrat Party, denied the charges and was granted bail.
The indictment came as protests against current PM Yingluck Shinawatra continued, and protesters briefly entered Government House.
Protest leader Suthep Thaugsuban, who was Abhisit Vejjajiva’s deputy in 2010, also faces charges but has asked the court to postpone his hearing.
Abhisit Vejjajiva and Suthep Thaugsuban were in power when thousands of supporters of ousted former leader Thaksin Shinawatra occupied parts of Bangkok. They authorized the army to clear the protesters.
The charges relate to the shooting deaths of a 43-year-old taxi driver and a 14-year-old during the crackdown.
Meanwhile, on Thursday, protesters briefly broke into Government House, and later cut off the office’s power supply, reports said.
Anti-government protesters want Yingluck Shinawatra to resign and for her government to be replaced with an unelected “People’s Council”.
They say that Thaksin Shinawatra, who is also Yingluck Shinawatra’s brother, controls the ruling Pheu Thai party.
Abhisit Vejjajiva and other Democrat Party lawmakers resigned from parliament on Sunday so that they could join the protesters.
On Monday, Yingluck Shinawatra dissolved parliament and announced general elections for February 2nd, 2014, as 150,000 protesters surrounded Government House.
However, she has refused to resign before the elections.
Yingluck Shinwatra’s Pheu Thai party has a majority in parliament, and draws significant support from Thailand’s rural areas. The party is seen as well-placed to win February’s election.
However, protesters accuse it of using public funds irresponsibly to secure votes, including on a controversial rice subsidy scheme which hurt Thailand’s exports.
Thaksin Shinwatra is in self-imposed exile after he was overthrown in a military coup in 2006 and convicted of corruption.
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