A federal jury in Washington found Clemens not guilty on two counts of perjury, three counts of making false statements and a single count of obstruction of Congress.
Clemens, 49, had been accused of lying to Congress in 2008 about taking performance-enhancing drugs.
The 354-game winner, who played for Boston, Toronto, the New York Yankees and Houston, was retried after U.S. District Judge Reggie Walton declared a mistrial in the case last July 14 after the prosecution presented evidence he deemed inadmissible.
Clemens became emotional while talking to reporters outside the Washington courthouse Monday, his eyes welling with tears as thanked his attorneys and those who supported him.
"I put a lot of hard work into that career," said Clemens, 49. "So, again, I appreciate my teammates that came in and all the e-mails and phone calls from my teammates."
The charges came in connection with Clemens' February 2008 testimony to a congressional panel probing the use of PEDs in baseball. He and other players had been implicated in doping by the Mitchell Report, an independent probe commissioned by Major League Baseball.
"It has been 4 1/2 years since we listened to a picture that doesn't match up with the man we've grown to know and love," Clemens attorney Rusty Hardin said, adding, "Justice won out."
Clemens was acquitted despite the testimony of former trainer Brian McNamee, who said he injected the seven-time Cy Young Award winner with steroids and human growth hormone.