In 2004, he was elected as senator. During his first term, he introduced at least 617 bills and resolutions and steered the passage of at least 16 bills either as principal sponsor or principal author.

On July 23, 2007, Estrada was elected as Senate president pro tempore.

On August 15, 2007, the Supreme Court voted 13-0 to uphold the Sandigabayan’s decision to grant his bail in connection with his plunder case before the graft court. On September 11, 2007 Estrada introduced Senate bill 1556, proposing to make ROTC mandatory for all college students.

In 2010, he was reelected as senator, finishing in the 2nd place. During the opening of the 15th Congress on July 26, 2010, he was reelected as Senate president pro tempore.