"In the long run" is an English idiom that refers to the a distant span of time during which some action will be taken. If this phrase is used, it means that the thing being discussed will not actually come to fruition until a lengthy amount of time has passed. As a matter of fact, the phrase "in the long run" is often used to contrast something that is happening in the short term. The implication is that the current activity will be temporary, while the action that is described using this phrase will have more of a permanent nature.
When a person uses an idiom, he or she is using a word or a short phrase in their speech as a means of adding some color and expressiveness to otherwise mundane descriptions. Idioms may have accepted meanings that are wildly divergent from what they meant when they were first used. They also can have meanings that are different from what the literal definitions of the words they contain might suggest. One such idiom denoting action happening in the distant future is the expression "in the long run."
If some action is described using this particular idiomatic expression, it means that the action will not actually take place for a long while. Other things may actually occur in the interim that can actually contrast the main action. Still, the phrase suggests that the action in question will eventually occur. For example, consider the phrase, "It may not happen for a while, but I believe that in the long run he will get the job."
This phrase is often used as a contradiction to action that is occurring either in the short term or in the present. When it is used in this manner, it is a way of saying that one thing that might be happening now will eventually give way or change into something that will happen in the future. As an example, someone might say, "While that other team might be in first place right now, I think that in the long run we will be crowned champions of the league."
Any time that the phrase is used in this way, it is implied that the action that will take place in the future will eventually supersede whatever might be happening closer to the present. The current action might hold sway for a certain period of time. Whatever happens "in the long run" though will have a more permanent effect.