When he was the head coach at East Carolina University, Steve Logan’s quarterbacks included Jeff Blake and David Garrard, who combined to play 26 seasons in the NFL.

As the offensive coordinator at Boston College, Logan mentored Falcons quarterback Matt Ryan, a three-time Pro Bowler. Now, in his first season as the 49ers quarterbacks coach, Logan’s top pupil is Colin Kaepernick.

“I’ve had an extraordinary run of luck, for lack of a better word, getting to coach some extraordinary young men,” Logan said. “And Colin is the next one. It’s a tall order. And I take it real seriously. But it’s a real gift as a teacher to get a student like this.”

Interestingly, here’s what Logan, 62, has told his student, a 27-year-old whose 2014 season suggested he’s not close to earning his graduate degree in QB: Let’s give you a lot less homework.

Logan and offensive coordinator Geep Chryst have taken a less-is-more approach with Kaepernick and the rest of the 49ers’ quarterbacks this offseason. Under Jim Harbaugh, the 49ers’ voluminous playbook could vex defenses … and the guy taking snaps.

At least that’s Logan’s view. Last year, as Kaepernick ranked 24th in the NFL in completion percentage (60.5) and 20th in passer rating (86.4), many observers saw an inaccurate quarterback struggling to see the field and work through his progressions.

Logan, however, thinks Kaepernick was too often executing plays he hadn’t come close to mastering. He says it wasn’t an issue of intelligence — he raves about Kaepernick’s “football IQ” — but information overload. And Chryst would know: He spent the previous four seasons as the 49ers’ quarterbacks coach.

“Coach Chryst might agree with me that it got way too spread out last year,” Logan said. “And it got a little bit to where maybe Colin didn’t know where that third read was. That was my feeling coming in here when I was visiting with Geep about how to move forward.”

In his first two seasons as a starter, Kaepernick had made vague references to the offense’s complexity. In the aftermath of a loss in New Orleans in 2013, for example, he was asked to account for the endless clock-management issues: “There’s a lot of things this offense has to do,” he said. “And it’s expected of us.”

The offense did a lot of nothing last year. The 49ers ranked 25th in points, allowed the third-most sacks in the league (52), led the NFL in delay-of-game penalties and scored just two offensive touchdowns in the fourth quarter.

Kaepernick has suggested this season’s thinner playbook could result in bigger production.

“It’s being able to execute the plays that are called and execute them more efficiently,” Kaepernick said. “I think with our new offensive coordinator, with our new quarterback coach, we’ve cleaned a lot of things up and made it more comfortable and friendly for players to be able to go out and make plays.”

The 49ers have scaled back the number of plays but disguised them in a variety of formations. And Logan says each play “behaves” differently depending on defensive coverages.

The 49ers hope it will allow Kaepernick to become intimately, run-it-in-his-sleep familiar with each play. It’s helped that the 49ers carried just three quarterbacks on their 90-man offseason roster and their practices were faster-paced than the sessions conducted under Harbaugh.

In other words, Kaepernick has had far more snaps with far fewer plays.

“The thing that we’ve all been trying to do is keep the offense compact, where it’s repetitive,” Logan said. “We’re changing the formation all the time, but we’re presenting the same package of plays over and over and over.

“Rather than football’s 101 best plays, we’re trying to have football’s best formations and packing it into an organized menu to where there’s constant repetition.”

The less-is-more approach has extended to other areas with Kaepernick, who spent the early part of his offseason in Phoenix refining his mechanics and studying video with two-time NFL MVP Kurt Warner and private coach Dennis Gile.

Did Logan confer with Warner and Gile? Nope. Did he discuss the program with Kaepernick?

“I’ve never mentioned it at all,” Logan said. “I just think you can have too many cooks in the kitchen on a thing like that.”

Logan is on the same page with wide receiver Anquan Boldin, 34, who said in the offseason his quarterback with a rocket arm and running back speed needed to “Go out and be Kap. … Trust your skills, trust your athletic ability that you have, and just go for it.”

Said Logan: “Those are really wise words from Anquan Boldin.”

It’s not that Logan is taking a just-go-out-and-play approach. A major point of emphasis with Kaepernick this offseason has been “discernment.” That is, discussing when it’s appropriate for Kaepernick to sprint downfield and when it’s best to hang in the pocket, read a defense and deliver a pass.

Stiil, Logan seems most intent on making sure Kaepernick trades confusion for comfort. And he’s optimistic his pupil entering his third full season as a starter is ready for his next exam.

“I think Colin might say there might have been some stuff that he wasn’t really comfortable with last year,” Logan said. “And I know he would tell you right now that he’s really comfortable.”

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com. Twitter: @Eric_Branch