Klaus signed the treaty hours after the constitutional court of the Czech Republic ruled it is in accordance with the country's constitution.
The Czech Republic is the remaining one country among the 27 EU members that has not yet ratified it. All countries have to ratify the treaty for it to enter into force, which the union wants by Jan. 1.
For the republic to ratify the treaty, only the signature of President Klaus was required.
Klaus, a Euro-skeptic, said earlier he would sign the Lisbon Treaty if the Czech Republic is exempt from the treaty's Charter of Fundamental Rights. Last week, EU leaders agreed to accept his demand.
Jose Manuel Barroso, president of the European Commission, told Reuters Television in Washington that the treaty could enter into force as early as December or January.