The Pashtun name, either boy or girl, must consist of two words:
The first name must be a typical Pashtun name and the last name must be the main tribe name, e.g. Muhammadzai, Isupzai, Marwat, Mohmand etc. So a complete name may be, for example, Turyalai Muhammadzai for boy, and Shaperai Isupzai for girl.
The history of the name "Khan" is quite vague but interesting. Historians claiming Turk or Arab descent claim that it is derived from "Kan" which means Lord of Warriors. Those that claim Jewish descent claim that it is derived from "Kahn", a title given to those Rabbi's who had the duty of giving animal sacrifices. Whatever its origins, Pashtoons give this title to somebody who is either a Chief, Leader, or a respectable person.
The "Khan" usage can be compared with the use of the "Turban". Pashtoons do not wear turbans unless they achieve a certain level of wisdom. The convention of Khan is similar. Hence there is no need to include "Khan" as the middle name.
A Full List of Names for both Boys and Girls are given Below: