Note: This is based off the latest manga scanned and translated by fans online and not the current manga in print. If you aren't up on the latest manga, this question contains spoilers.
Kakashi activated his mangekyou sharingan back in the war times when
he killed Rin,
but he didn't use it for such a long time.
What was the reason?
Although his personal reasons are of course never revealed, and more than likely are due to plot reasons there are practical reasons why one wouldn't just use an ability like that all the time.
It's use deteriorates your eyesight to the point of blindness. If you don't need it don't use it.
The above is the first link that comes up when you google "Mangekyo Sharingan". Quotation:
Over time, use of the Mangekyō Sharingan's techniques deteriorates the user's eyesight to the point of blindness.
EDIT
If the OP meant to ask about Kakashi, it is most likely due to what Sunpech said, the plot wasn't all there yet. Plus, consider how draining the use of the standard sharingan was on Kakashi near the beginning of the series. The strain rendered him bed-ridden due to prolonged usage. The mangekyo variant is far more draining than the base situation.
The sharingan itself was something Kakashi used very sparingly, it only follows that the far more dangerous mangekyo would be used far less.
I would argue that Kakashi was simply unaware of having a Mangekyo Sharingan, or of having anything but the regular three-tomoed Sharingan, up until the time skip.
First and foremost, we know from the manga that Kakashi develops Kamui during the time skip: when he meets Naruto and Sakura after the time skip (chapter 247), he refers to a new techinque that he has developed recently. Naruto and Sakura dismiss him over a distraction without letting him elaborate, but it is later revealed in chapters 275 and 276 that the technique is Kamui.
A plausible in-world explanation, which was my understanding while I was reading, is that he underwent some Sharingan-specific training during the time skip in order to counter the increasing threat posed by Akatsuki, specifically Itachi Uchiha. During that training he discovered that, for some reason (could have been Rin, but for all he knew at the time it could have been Obito), he could use Mangekyo Sharingan.
To my knowledge, there is no indication of Kakashi ever considering having Mangekyo Sharingan, let alone consciously activating it for purposes other than Kamui, before the events of 275: it activated on its own upon Rin's death, Kakashi collapsed right after and that was it.
It should be mentioned for context that pre-Shippuden Kakashi knows, although possibly without too many details, that Mangekyo Sharingan is a thing. This can be seen in chapter 142, when he foresees that Itachi is about to use it against him, Asuma and Kurenai. It isn't all too surprising, considering that it does not seem to be a secret (Fugaku Uchiha mentions it to baby Sasuke in a flashback in chapter 224) and that it has a bearing in recent history.
