Methods of making vacuum insulated glass (VIG) window units are provided, including activating getters in a process of making VIG window units. In certain example embodiments, at least one getter is activated during and/or at the end of a pump-out/evacuation process in which the cavity between the substrates is evacuated. In certain example embodiments, the getter(s) may be activated (e.g., by at least a laser beam that is directed through a pump-out tube) during and/or at the end of the evacuation process in which the cavity between the substrates is evacuated to a low pressure that is below atmospheric pressure.