Does the insomnia side effect of fluoxetine go away after a while? or will i have insomnia problems until the treatment is over?

It depends: You did not say how long you have been on this drug, or how you are affected (difficult falling or staying asleep, frequent awakenings, etc). Most significant is that sleeplessness may worsen the reason you began fluoxetine in the first place. Discuss this with the doc who prescribed it to determine if you should remain on it or change to a different product.

Take in am: Insomnia caused by fluoxetine is most commonly alleviated by taking it in the am. If you are takig it in the am an still have insomnia a different med is probably indicated