Still, he was on the winning end of an 11-4 Hammerheads victory over the St. Lucie Mets at Roger Dean Stadium.
Afterwards, the upbeat right-hander made his intentions clear.
"I want to get to the big leagues soon. Everybody does," Fernandez said. "But I don't want to get rushed. I want to get there. I want to stay there. I don't want to get there and come back down. I want to get there and play for 12 to 15 years. That's what I want to do. That's my goal."
Meeting challenges is nothing new for Fernandez.
Born in Cuba, Fernandez once spent a year in jail for attempting to flee his native country. The time in prison, however, didn't deter his desire to seek a better way of life.
At age 15, he arrived in the United States, entering the country through Mexico after he defected.
"Every player has some history," Fernandez said. "I went through a lot of rough stuff when I was young. Sometimes, not having nothing to eat. Sometimes, it was going out there with no shoes. I had like two T-shirts to go out. Just little things.
"My mom and grandma have been amazing. They worked their butt off to get me food, and to help me be a good baseball player. They've been amazing. Now I'm here and getting my dream."
Eventually, he made it to the United States, where he attended Alonso High School in Tampa.
"When I came here, I didn't know anything," Fernandez said. "My English was like, bad. I couldn't say anything. I started going to school, taking English classes. I try a lot. I try to speak more English than Spanish."
On June 6, 2011, the Marlins selected Fernandez with the 14th overall pick in the First-Year Player Draft.
Now, he is a level of professional ball closer to his big league dream.
"Obviously, it's a remarkable story," Jupiter manager Andy Haines said. "I don't think anybody that hasn't been through that can even fathom what that guy has been through. I can't even pretend to understand, I kind of get bits and pieces. He's certainly a mature kid who wants to learn."
Often at the Minor League levels, promotions are made out of necessity, sometimes due to a lack of depth in the system. There might be an injury, and a prospect could be pushed along, even if he isn't totally ready.
In Fernandez's case, reaching the next step was earned. At low Class A Greensboro, the hard-throwing right-hander was simply dominant. Armed with a 97-mph fastball, he was 7-0 with a 1.59 ERA in 14 starts.
Hitters in the South Atlantic League were simply overmatched, displayed by Fernandez's 99 strikeouts in 79 innings and opponents' .189 batting average against him.
"For the most part, he wasn't being challenged," said Marty Scott, the Marlins' vice president of player development. "In my opinion, he was close to domination down there, with his record and the numbers he put up."
If projections hold true, Fernandez is the real deal, a legitimate future ace at the big league level.
Fernandez's fast rise has also earned him a spot on the World roster for the July 8 Futures Game at Kansas City.
Miami's top two prospects will be heading to the Futures Game. Fernandez will be joined by outfielder Christian Yelich, his Jupiter teammate, who will play for the United States squad.
Yelich provided a big boost for Fernandez and the Hammerheads on Thursday. The outfielder had four hits and two homers, including a grand slam, and seven RBIs.
What Fernandez needs to do at Jupiter is allow his talents to naturally progress. He turns 20 on July 31, and a solid second half should make him a strong candidate to reach Double-A Jacksonville at the start of the 2013 season.
For now, he is trying to make an impact with the Hammerheads.
Fernandez's fastball is clearly there, repeatedly being clocked in the mid-to-upper 90s. He also throws a slider and curveball. The pitch the organization wants Fernandez to develop is his changeup.
"He can get away with his fastball because of its velocity," Scott said. "But his main emphasis, as far as from a development standpoint, is utilizing his changeup more. We've seen it where guys can get away with their fastball in the Minor Leagues. But when they get to the big leagues, they've got to locate a little better and change speeds a little better. That's the main emphasis."
As the second half of the Minor League season moves along, the Marlins will be closely monitoring how many innings Fernandez throws. He's already at 79, and the team plans on capping him around 150.
The plan the rest of the year is to pitch Fernandez no more than five innings, unless his pitch count is low.
"We're trying to get him through the year," Haines said. "He's not going to go seven or eight innings the rest of the year. When you've got an arm like that, there are only so many bullets in there. We're certainly not going to take a chance.
"I think the goal is, you want to let him go out and compete and let him try to win the game. That makes him go. At the same time, we've got to watch those innings. We're going to keep him around five."