To join the fight  in a Clan War, you must be part of a clan when a Leader or Co-leader presses the 'Start War' button. If you join the Clan after a war has begun, you’re able to spectate but not participate.

Also, if the two clans chosen are only roughly the same size, then clan members with the lowest trophy counts will be excluded from the fight. This is to make sure the war is fought between an even number of War Bases, and to balance out the odds.