Judge Raner C. Collins of the Federal District Court in Tucson declared the trial of Scott Warren over after jurors in the case could not reach a verdict following three days of deliberations.
Warren, a 36-year-old geography teacher and long-time volunteer with the humanitarian group No More Deaths, had been accused of conspiring to smuggle two men from Central America who crossed the border illegally in 2018 and sought refuge at one of the NGO's bases.
He had faced 20 years in prison if convicted.
Prosecutors contended during the two-week trial that Warren had conspired with a nurse and the operator of a migrant shelter called the Barn, located about 110 miles (177 kilometers) from Tucson, to smuggle the two migrants and shield them from the Border Patrol.
Warren's defense lawyers, however, argued that their client was simply trying to show "basic human kindness" when he assisted the two men and that he was targeted by authorities after No More Deaths released a video showing Border Patrol agents destroying water jugs left by the group in the desert to assist migrants.
The case, which drew international attention and prompted vigils across the United States, was widely seen as a test of how far the Trump administration was willing to go in its battle to deter illegal immigration.
In a statement on Twitter, No More Deaths said the judge's decision to declare a mistrial showed that "the government has failed in its attempt to apply federal charges to acts of common compassion."
"In Scott's own words, 'Today it remains as necessary as ever for local residents and humanitarian aid volunteers to stand in solidarity with migrants and refugees,'" the statement added.
Amnesty International and United Nations human rights representatives had urged that all charges against Warren be dropped, saying that providing humanitarian aid could not be considered a crime.
"The vital and legitimate humanitarian work of Scott Warren and No More Deaths upholds the right to life and prevents the deaths of migrants and asylum seekers at the US-Mexican border," the UN experts said in a statement last week.
"The prosecution of Scott Warren represents an unacceptable escalation of existing patterns criminalizing migrant rights defenders along the migrant caravan routes."
Warren faces misdemeanor charges in a separate case related to leaving water jugs and food for migrants in 2017 at the Cabeza Prieta National Wildlife Refuge west of Tucson.
He is awaiting a verdict in that case.