This study reviews the use of magnetic and electromagnetic fields (EMF), pulsed electromagnetic fields (PEMF), and transcranial magnetic stimulation (TMS) in Parkinson’s disease, Alzheimer’s disease (AD), or Multiple Sclerosis (MS). The Introduction provides a review of EMF, PEMF, and TMS based on clinical observations. This is followed by a description of the basic principles of these treatments and a literature review on possible mechanisms describing the coupling of these treatments with biological responses. These response mechanisms include the cell membrane and its embedded receptors, channels and pumps, as well as signaling cascades within the cell and links to cell organelles. We also discuss the magnetic contribution to coupling EMF, as well as the recent finding of cryptochrome as a putative magnetosensor. Our conclusion summarizes the complex network of causal factors elicited by EMF such as those arising from the cell membrane via signaling cascades to radical oxygen species, nitric oxide, growth factors, cryptochromes and other mechanisms involving epigenetic and genetic changes.