"I don't view this as leaving the Republican Party as much as the Republican Party leaving me," the former two-term New Mexico governor said at an event at the state Capitol in Santa Fe.
Johnson's campaign lacked the resources and media attention of other Republicans, though he did manage to qualify for three of the 13 televised debates so far.
After outlining a strategy to win the nomination based on a strong showing in the New Hampshire primary, he nearly missed the deadline to qualify, scrambling to arrange an overnight flight to get to the Statehouse on the final day of the filing period.
Johnson is best known for advocating the legalization of marijuana. He joked Wednesday that in order to sustain a campaign effort, he had hoped to raise $1 from each of the 100 million Americans he claims have smoked marijuana.
"But that hasn't worked out," he said.
Having been largely ignored in his former party, Johnson said that running as a Libertarian would give him a chance to keep his message alive.
"We are fed up with the two-party system. And the ability to be in the game, to be on the ballot in all 50 states is an opportunity to advance this message that resonates with most people in this country," he said.
Mark Hinkle, the national Libertarian Party chairman, joined Johnson for his announcement. But Johnson is now the 10th individual to announce plans to run for the party's nomination.
A spokesman said the nominee will be chosen at the party's national convention in May.