Now he's presumably in his last days with the Dons, ready to walk away as a 6-foot-4, 220-pound pitcher with a few million bucks in his pocket and the Major Leagues in the not-too-distant future.
"It's been great to see the transformation," USF coach Nino Giarratano said. "Kyle has put in all the work. He deserves all the credit."
The transformation has turned the right-handed Zimmer into one of the players considered to be a candidate to be taken with the first overall pick of the First-Year Player Draft, which begins June 4.
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"It's been a little crazy," said the 20-year-old Zimmer. "It's a little hectic hearing my name all over the place like that, but I'm just trying to keep blinders on and focus on what I can control, making pitches and trying to do what I can to help the team."
A Major League crosschecker who has seen Zimmer several times over the past two seasons said the hype is warranted.
"He's really good," he said. "He at times will pitch with four above-average Major League pitches. ... He's got some adjustments he needs to make in his delivery, but his pure stuff is Major League ready right now."
Heady stuff for a kid who three years ago barely attracted the attention of pro scouts as a skinny infielder at La Jolla High, just north of San Diego. Zimmer went to USF as third baseman, having hit .410 with four homers in his senior year of high school. Zimmer had pitched in high school, but only as an afterthought.
"I'd get on the mound and throw some innings here and there to help the team out, but I never really had any interest in it till I got up here," Zimmer says.
When Zimmer arrived on the picturesque campus on a hill in San Francisco, there was another third baseman there. Stephen Yarrow was one of the Dons' best hitters and signed with the Giants as a non-drafted free agent last season.
Without a spot for Zimmer at his preferred position, Giarratano and pitching coach Greg Moore went to the plan they'd held all along for him. They put him on the mound.
"In 2008 Kyle was at a camp and my assistant called me and said, 'We saw this kid from San Diego that's got a rifle arm,'" Giarratano said. "We got him to play third base, but we thought eventually he might be able to pitch. From Day 1, we always had some idea pitching might be in his future."
That future arrived in Zimmer's freshman year. He got on the mound for just 5 1/3 innings, but he struck out seven. He was raw, but there was enough there that coaches convinced him to devote himself to pitching.
"It was a little frustrating at first," Zimmer said. "I hadn't thought of myself as a pitcher. I wanted to hit and stuff like that. They said, 'We want you to focus on this, because we see potential.' I took it as another challenge and started working every day and started to see some improvement."
Zimmer spent the summer after his freshman year working on his delivery, working in the weight room, learning the finer points of gripping the ball.
He also grew.
With weight training and a growth spurt that filled out his body in all directions, Zimmer was transforming from the skinny kid to a fully grown man on the mound. The added size and improved flexibility helped Zimmer increase his velocity. His fastball jumped from 88-90 mph to the mid- to upper-90s. By the end of his sophomore season, he had climbed from the bottom to the top of the USF rotation.
Last spring, he outdueled UCLA's Gerrit Cole -- the No. 1 overall pick in the 2011 Draft -- in a memorable NCAA playoff game. Zimmer pitched a four-hit shutout, with 11 strikeouts, in a 3-0 victory over the No. 12 Bruins.
"That was a lot of fun," Zimmer said. "I was treating it like another start. I knew we were going against the best pitcher in the country. I knew I wouldn't have room to make mistakes. I just tried to stay with that sharpened awareness and execute my pitches."
Said the crosschecker: "That was his coming out party. He was outstanding."
Zimmer then pitched in the Cape Cod League and impressed the scouts even more. When he came out this season touching 99 mph, he climbed to the top of Draft boards.
Heading into his final regular-season start on Friday at St. Mary's, Zimmer sported a 2.59 ERA and 96 strikeouts and 15 walks in 83 1/3 innings.
"He hasn't even reached his full potential yet," Giarratano said. "He's just now learning all the little things. He's going to keep getting better."
Zimmer already has developed some of the finer points of pitching. Besides his above-average fastball, he's got an outstanding 12-to-6 curve that he uses as a swing-and-miss pitch. He throws two sliders, one to keep in the strike zone and one with more bite that drops into the dirt. He also has a changeup.
Giarratano also loves his makeup.
"He's got great leadership qualities," Giarratano said. "He's a great kid, a great competitor. He can pitch deep into games. He can handle when people score against him. He's not afraid to pitch behind in the count. He's not worried about any of the things he can't control. He just controls himself. The bigger the stage, the better he does."
The stage is about to get even bigger for Zimmer. When Draft day comes, his name may be the first one called.
"I always had confidence in myself and felt like I could be here," Zimmer said. "It's been a process. It's taken some long days in the weight room and at the field. It's been a lot of hard work. It's great to see it all pay off."
Jeff Fletcher is a contributor to MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.