The verdict, reached by a jury in U.S. District Court, was the second trial for 37-year-old Scott Warren after a previous jury in June deadlocked on harboring charges.
Warren’s defense attorney, Greg Kuykendall, praised the jury’s decision.
"They parsed the evidence," he said. "They paid rapt attention while we were putting on our defense and while the prosecution was putting on its case, and they decided that humanitarian aid is not always a crime, the way the government wanted it to be."
Warren has denied being politically motivated or helping migrants hide or avoid authorities.
U.S. agents arrested Warren in January 2018 at a humanitarian aid station in Ajo, Ariz. – known as “The Barn” – where two Central American men had been staying for several days.
A prosecutor questioned Warren's claim that he was only "orienting" them before they left the camp.
The camp is run by “No More Deaths,” a border activist group that tries to prevent immigrants from dying in the desert.
Warren said the group's training does not advise migrants on how to avoid authorities. He said his interest is in saving lives.
Michael Bailey, the U.S. attorney for Arizona, expressed disappointed in Wednesday but vowed to continue prosecuting people who harbor and smuggle immigrants and those who sneak across the border.
He said he wouldn’t distinguish between someone who is “trafficking or harboring for money,” or motivated by “a misguided sense of social justice.”
Warren and his supporters have accused the Trump administration of scrutinizing humanitarian groups. The federal judge overseeing Warren’s re-trial banned him from mentioning President Trump on the grounds of keeping the trial apolitical.
Thousands of immigrants have died crossing the border since the mid-1990s, when increased enforcement pushed many to Arizona's scorching desert.
The Associated Press contributed to this report.