Although he was expected to compete for the center field job in 2006, Logan was beaten out by Curtis Granderson and was subsequently injured upon arrival in the minors. On August 29, 2006, Logan was designated for assignment by the Tigers. On September 1 of that year, he was traded to the Washington Nationals, after asking Detroit management for a trade. Upon arriving in Washington, Logan immediately impressed with his spectacular catches and speed. Indeed, Logan was recognized that year as the fastest player in Major League Baseball. He ended up hitting .300 and making several breathtaking catches in the field.

In 2007, Logan started off the season as the opening day center fielder for the Washington Nationals. He injured his foot on that same day after crashing into the wall in the outfield. He would be out injured for over a month but ended up hitting .265 after slumping toward the tail end of the season. Logan's lack of power prompted the Nationals to look for a power hitting outfielder to replace him at season's end. Logan was not offered a new contract by the Nationals and became a free agent on December 12, 2007.

On December 13, 2007, Logan was identified in the Mitchell Report as a client of Kirk Radomski, who distributed banned performance-enhancing substances to MLB players. He would later admit that he used Human Growth Hormone (HGH), a legal substance, banned by Major League Baseball, in order to recover from his injury in the minor leagues.