Johnson told a news conference at the state Capitol that the decision was difficult but that he "was deeply disappointed by the treatment I received in the Republican nomination process."
Johnson has been excluded from all but two GOP presidential debates. He also has barely registered in the polls.
The former two-term governor said that if he earns the Libertarian Party's presidential nomination, he will appear on the ballots in all 50 states and will not be "held hostage to a system rigged for the wealthiest and best-known candidates in a handful of states who happen to have early primaries."
Johnson is fiscally conservative but supports such liberal causes as legalizing marijuana and abortion rights.