If a PC is 'surprised,' (PHB p 189) he/she cannot take a reaction until the turn ends. Given that Surprise is determined at the start of combat, i.e. before any turns have happened, how could you have had a reaction prepared anyway?
There are abilities/actions that use "reactions" that don't need to be prepared. Opportunity attacks are attacks that use your reaction, but don't have to be prepared before it is taken. You just get to decide if you want to use your reaction to make an opportunity attack when/if an enemy leaves themselves open for one.
There are also some spells (the 1st level Shield being the one that comes to mind first) that use a reaction to cast. When an enemy hits you, you can cast the Shield spell as a reaction and you don't have to decide that unless the enemy gets a successful attack on you.
So being surprised means you can't take those actions on the first round of combat until after your turn during that round has ended. (When surprised, you still have a turn in initiative; you're simply unable to act during that round.)
As for a prepared reaction, what you might be thinking of is the conclusion of a "readied action". A readied action is where you use your action to state what you will do when a discernible trigger happens. When that trigger happens, then you use your "reaction" to perform the previously stated action. Since you don't get a turn to make a "readied action", not getting a "reaction" doesn't come into play.