A new committee must now be appointed to write another draft, further setting back elections.
The draft has been widely criticized, in particular a clause which enables a 23-member panel to take over government during a “national crisis”.
Thailand’s army ousted the elected government after months of political unrest.
The 247-member National Reform Council rejected the draft charter by 135 votes to 105, with seven abstentions.
Correspondents say that it met strong opposition on practically all sides of the political divide.
Another committee will have 180 days to write a new one, which will later be put to a nationwide referendum.
Until a new constitution can be drafted, the military government retains its substantial powers.
It had said elections could take place in late 2016, but analysts say the delay means 2017 is more likely.
Critics of the draft constitution say it would erode the power of political parties in favor of the army and prevent a genuine democracy from being established.
Thailand has seen numerous different constitutions since the end of the absolute monarchy in 1932.
For years Thailand has been divided between pro-democracy parties that support former PM Thaksin Shinawatra, and an alliance of conservatives, including members of the military, the judiciary and royalists.
Thaksin Shinawatra’s allies have prevailed in every election since 2001, but have faced two coups and the removal of three prime ministers by the courts.
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