The sentence was handed down in U.S. District Court in Seattle after Harris-Moore pleaded guilty to federal charges.
The federal prison term will be served concurrently with a seven-year sentence handed down earlier in Island County Superior Court, after Harris-Moore pleaded guilty to dozens of state charges.
Harris-Moore, 20, gained international notoriety while evading police across the country in stolen planes, boats and cars during a two-year crime spree.
He sometimes committed his burglaries and thefts without shoes, earning him the nickname "Barefoot Bandit." Fans followed him on Facebook, many of them urging him to continue his brazen crimes.
At Friday's sentencing hearing, Harris-Moore addressed the court for the first time.
He apologized to his victims, saying, "I now know a crime that took place overnight will take years to recover from," the 20-year-old said in court.
He particularly apologized for stealing planes, saying his arrogance led him to keep alive his dream of flying.
"What I did could be called daring, but it is no stretch of the imagination to say that am lucky to be alive ... absolutely lucky," he said. "I should have died years ago."
He promised to make restitution to his multiple victims, and Judge Richard Jones ordered him to do so, with the amount to be determined at another hearing in about a month.
His daring run from the law earned him a movie deal to help repay his victims after he flew a stolen plane from Indiana to the Bahamas in July 2010, crash-landed it near a mangrove swamp and was arrested by Bahamian authorities in a hail of bullets.
In court Friday, the judge asked Harris-Moore to speak to young people who may look up to him because of his exploits.
"I would say to younger people they should focus on their education, which is what I am doing right now," he said. "I want to start a company. I want to make a difference in this world, legally."
Federal prosecutors had asked for Jones to impose a 6 1/2 year sentence to be served while Harris-Moore serves his state time. His attorneys had asked for a federal sentence of just under six years.
The judge acknowledged that Harris-Moore had a difficult childhood, one with "complete lack of parental guidance" and alcohol abuse. But he said he was concerned that that his previous court appearances didn't have an impact on him.
Jones acknowledged that Harris-Moore committed his early crimes to survive after fleeing from home. But he said "most of the federal offenses were committed for one reason: to fulfill your passion for flying at all costs and consequences."
The judge encouraged Harris-Moore to get treatment in prison.
"The most important day in your life is what you do when you are released. It will be up to you to create a new flight plan," Jones said.
Harris-Moore's mother attended the hearing. Pam Harris Kohler took a couple of swings at news photographers outside the federal courthouse after the sentencing but missed.
One of Harris-Moore's attorneys said the young man wrote a letter to his mother, whom he has refused to see in jail, before he was sentenced.
Watch the raw video of Harris-Moore's mother taking swings at the media: