Dykstra was the 23rd pick in this year's First-Year Player Draft and played his collegiate ball at Wake Forest University. But he is a hometown kid, having played his high school baseball at Rancho Bernardo High School.
"We are extremely excited that we were able to reach an agreement with Allan Dykstra this evening," said Padres director of scouting Bill Gayton. "It came down to the last hour. We spoke earlier this afternoon, and we had some conversations that obviously picked up as we neared the signing deadline."
Dykstra was given a $1.15 million signing bonus.
The major hang up with the negotiations came after a team examination raised questions about a hip surgery Dykstra had during his days at Rancho Bernardo.
The examination revealed some issues with Dykstra's hip, the same one that he had surgery on in high school. He'd developed avascular necrosis, a degenerative hip condition.
But Towers expressed that the deciding factor in going ahead with signing Dykstra was that his hip issues didn't prevent him from playing collegiately for the last three years. After feeling comfortable with what his doctors and the Padres' doctors had to say about his hip, the Padres were able to get the deal done.
"Allan had a strong desire to play for the Padres," Gayton said. "It was his favorite team, his hometown team and we selected him No. 23 overall, so we certainly didn't want to run into long-term problems from an organizational standpoint. I mean, you have an extremely talented individual that, hopefully long-term, has a very successful career and we reap the benefits and he does as well."
Now that he's signed, Dykstra and the Padres can focus on getting him back into the flow of baseball. When Dykstra was drafted, his college season was already complete as the Demon Deacons did not make the postseason, so he hasn't been playing competitive baseball for quite some time.
"He certainly missed some time this summer to get a chance to play [with Class A Eugene]," Towers said. "But the key thing is that we got it done and I think it just adds to an already very good 2008 Draft. And now it makes it all that more successful, having Dykstra now as a part of the Padres family."
Dykstra, who hit .323 with 16 home runs and 50 RBIs for the Demon Deacons, is someone the Padres are excited about getting into PETCO Park.
"He has the type of power that plays at PETCO," Towers said. "This ballpark certainly won't be able to hold him. It's hard to find those types of players out there."
Dykstra will be sent to Eugene upon his arrival but will tentatively arrive at PETCO on Sunday.
"You want to introduce him to professional baseball," Gayton said. "You'd like him to interact with his teammates and get a feel for the organization, staff and players that are here and are going to be working with him. Hopefully, he'll be playing with them for many years."
Ronald Clark is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.