You can apply during the time you are taking your prereqs. As long as you finish your classes before matriculation into your accepted pharmacy school, then you're good. However, some think it is better to have completed at least some of your higher-level classes (Organic I, Calculus, A&P) before applying. Also, some schools allow students to take classes during the summer before admission, and other don't...so look into your desired schools to find out more info.
Hope that helps!