Josh Johnson has yet to throw a pitch for the Padres. It is unclear if he ever will.

The right-hander will undergo his second Tommy John surgery Thursday. The procedure will be performed in Pensacola, Fla., by Dr. James Andrews. An exam by the noted orthopedic surgeon earlier this week revealed damage to the ulnar collateral ligament in Johnson’s throwing elbow.

“It’s a big loss,” said Padres Assistant General Manager A.J. Hinch. “He unfortunately never got off the ground, other than a few spring training starts. We all feel badly for JJ.”

Johnson will miss all of the 2014 season and some of 2015. Besides ranking as the latest and most significant blow to the Padres’ pitching depth, it is a dreaded repeat of history for the pitcher himself. Andrews performed Johnson’s first Tommy John surgery in 2007 and a cleanup procedure in October, removing bone spurs from Johnson’s right elbow.

In November, the Padres signed Johnson to a one-year, $8 million deal. At the time, it was viewed as a potential bargain for a pitcher with a career 3.40 ERA and an impressive, if often interrupted, track record. Acknowledging the risk, General Manager Josh Byrnes negotiated a club option for $4 million should Johnson make fewer than seven starts in 2014.

Now that the scenario has become worst-case, the Padres will have an important determination to make at the end of the season.