"Auf Dauer läuft er nicht."
In the long run often refers to the ambiguous future in which events turn out to be this way or that way....
"he doesn't run in the long term" probably means that there is an irreversible damage to his body and that he could never be able to run again. Or he was considering the race for a long time but in the end he didn't as philster043 points out.
Still it's not a natural translation.