in the long run

eventually; over or after a long time

the distant future, in the end

For now he is losing money on his stocks but in the long run he should make money.

(from Idioms in Speech)

eventually; before all is over; finally; after many changes of fortune, successes and failures

He filled a pipe and tried his best to feel that, after all, in the long run Dinny would be happier unmarried to him. (J. Galsworthy)

"Naturally I don't approve of them," said Emery, still uncertain whether he felt more annoyed or pleased at Clayton's insistence that in the long run they were both good fellows more or less on the same side. (J. Lindsay)

Hospital meant charring as far as work went but in its social atmosphere it meant something more interesting, more romantic, and, in the long run, more respectable. (J. Wain)

Note: In the long run means 'over a period of time' or 'at the end of a long period of time'. In the end means 'something less vague'. It is a more particular point of time.

In the long run it will not matter to us whether we stay at Brighton or Hastings. They are both seaside towns so I cannot understand why my parents are making such a fuss about the choice.

But:

In the end we decided to stay at Brighton because my mother said there was more to do there if it rained. I must tell him about it in the end.