This can be done overtime, as in through your playthrough. You do not need to repeat a mission.
To gain this achievement, you need to make sure you are not spotted and the enemy has to have their back turned. It is preferred that you crouch instead of standing, because if you stand, they can hear you and will draw out their weapon. That being said, get into a crouching position and make your way towards them as they are standing or walking around. Some will even sitting at their desk. Once you reach that point, the game will tell you that it is OK to subdue them. To do so, just press down the right thumbstick and the animation will begin and then end quickly.
If you go through the story, you'll rank up these kills in no time and the achievement should pop up. Good luck!