A military court had sentenced Behenna to 25 years in prison but his sentence was later reduced to 15 years and he was granted parole as soon as he was eligible.
The case attracted broad support from the military, Oklahoma elected officials and the public, according to White House Press Secretary Sarah Sanders.
She added Behenna was a model prisoner while serving his sentence, stating "in light of these facts, Mr Behenna is entirely deserving" of the pardon.
Two Republican senators from Oklahoma hailed the pardon and thanked President Trump for giving Behenna "a clean slate."
Behenna acknowledged during his trial that instead of taking the prisoner home as he was ordered, he took the man to a railroad culvert, stripped him, and then questioned him at gunpoint about a roadside bombing that had killed two members of his platoon.
Behenna said the man moved towards him and he shot him because he thought he would try to take his gun.
Oklahoma's attorney general first requested a pardon for Behenna in February 2018 and renewed his request last month.
Attorney General Mike Hunter said he believed Behenna's conviction was unjustified because of erroneous jury instructions and the failure of prosecutors to turn over evidence supporting a self-defence claim.