Murphy spent the last two seasons managing the Padres short-season affiliate in Eugene.
"He's had the best record in the Northwest League the last two years and creates a good environment," said Randy Smith, the Padres vice president of player development and international scouting.
"He expects a lot, but he makes it fun."
Murphy, 53, was first hired by the Padres in 2010 as a special assistant. He compiled a 93-47 record in his two seasons in Eugene.
"I loved the combination of his intensity and his ability to keep the daily grind fun," said Maxx Tissenbaum, an infielder in 2012 for Eugene and an 11th-round pick in 2012. "He demands that every guy is always working hard but understands the routine of playing every day can get repetitive. He's a guy who you can really tell cares about the guys. He's someone you want to play for."
Murphy made his mark in the college ranks, where he won 318 games as Notre Dame head coach from 1988-1994. He then guided Arizona State to 10 consecutive postseason appearances and 12 in his 15 seasons with the Sun Devils.
He was the Pac-10 coach of the year four times and took the Sun Devils to the College World Series four times (1998, 2005, '07 and '09). Murphy posted a 629-284-1 record in Tempe.
"His success rate is just phenomenal," Smith said. "I think he's learned a lot about the difference in the college game and pro ball. He's very bright."
Tucson will also have a new pitching coach in Bronswell Patrick, who served in the same capacity with Single-A Lake Elsinore in 2012. Tom Tornincasa will take over as hitting coach. He spent the last three seasons working with hitters at Double-A San Antonio.
In September, the Padres announced that Tucson manager Terry Kennedy would not be returning for a fourth season. Pitching coach Steve Webber was also informed he wouldn't have his contract renewed.
Tucson finished 56-88 this past season, 30 games out of first place in the Southern Division of the Pacific Coast League. The team used 25 different starting pitchers during the season.