The right-hander arrived in Pittsburgh in 2004 touted as the organization's No. 1 prospect, only to find himself having reconstructive surgery on his left shoulder that October.
Three months later, he went back under the surgical lights, this time to have surgery performed on his right shoulder, which then kept him out of baseball for over a year and a half.
But everything that he had gone through, everything that he had overcome, all culminated when he took the mound on Saturday. At the age of 27, Van Benschoten was back.
"It really means a lot [to be here]," he said afterward. "Three years, it's worth the wait."
He wasn't the only one who thought so.
His fill-in manager called him "outstanding", the sellout crowd of 36,610 treated him to a standing ovation as he left the mound in the sixth and his teammates were left shaking their heads at how a pitcher who has been through so much could make such an impression in his return.
"Johnny threw great for his first time back in what, three years?" said Adam LaRoche, who scored the Pirates' only run of the night. "Pretty unbelievable."
Yes, Van Benschoten came away losing the duel to Chicago's Mark Buehrle, after allowing two runs in his 5 2/3 innings of work. But the Pittsburgh right-hander wasn't about to dwell on losing a hard-fought game. He came away with confidence, shutting the door on a painful past and opening the door to a bright future that is still glowing, despite being a few years behind schedule.
"I was just glad my arm stayed through it," Van Benschoten said. "Health-wise, that's about the only thing I was worried about. It was big for the health issue to close the door and be able to get here again."
Two runs scored off the Pirates starter in the second, although a clean throw from LaRoche likely would have prevented the White Sox from scoring off Van Benschoten at all.
LaRoche handled a Rob Mackowiak ground ball in the second inning, stepped on first but then fired a throw over the head of catcher Ryan Doumit trying to stop Jermaine Dye from scoring from third.
An on-target throw would have had Dye at the plate and ended the inning, but instead, the right fielder scored and White Sox third baseman Josh Fields followed with an RBI double to give Chicago a two-run lead.
From there, Van Benschoten allowed only one baserunner through the next three frames before exiting the game at the 90-pitch mark with two runners on in the sixth.
"He just wanted to go out there and compete today," said bench coach Jim Lett, who is serving as manager while Jim Tracy is attending his son's graduation ceremony this weekend in California. "It's been a while since he's been here and he wanted to say, 'Hey, I belong here.' And he did that today."
About the only thing Van Benschoten didn't accomplish on this night was what he did best as a standout hitter at Kent State University -- drive in runs. Twice the pitcher came to the plate with runners at the corners, but both times was unable to get the ball further than the pitcher's mound.
Though he wasn't even about to let that damper his night.
"I'll probably think about it tomorrow," the right-hander said. "I didn't think about it at the time, but they were definitely out there for me. That was unfortunate."
The rest of the offense wasn't much better, recording nine hits off Buehrle, but scoring only a lone second-inning run and leaving eight runners stranded.
"It's the clutch hits," said LaRoche, who collected three hits off Buehrle. "It's a lot easier said than done, especially in times like tonight. All of a sudden, you get guys on and then you're over-swinging, trying to get them home."
And unfortunately for the Pirates, the bullpen's success was no better than that of the offense with runners on base. While the Pirates have to be encouraged by another strong starting performance, the night unfortunately highlighted the ineffectiveness of the Pittsburgh bullpen yet again.
None of the three Pirates relievers who pitched on Saturday escaped unscathed as the Pirates saw a manageable one-run deficit balloon to five quite rapidly after Van Benschoten's exit.
John Grabow allowed a home run to Fields, who had only gone deep one other time in his short career. Dan Kolb couldn't pitch a scoreless eighth, allowing his second run in as many appearances since being called up from Triple-A Indianapolis. And Tony Armas followed the next inning, allowing two doubles that pushed the Chicago lead to five.
But as the hitters go home mulling lost opportunities and the relievers shake their heads at another tough day at the park, at least one Pirate left the park with a grin and a sigh of relief.
Van Benschoten didn't mind being surrounded by tape recorders and notepads after the game. As he put it: "This means you're doing something, rather than, 'So you're in the surgery room again', it's better than that."
Better for the Pirates, and better for a pitcher who finally knows he once again has what it takes.
Jenifer Langosch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.