Because the mind and body are a single system, changing our brainwaves and spending more time in harmonious, relaxed, and restorative mind-states also affects our physical health. Physical health then reinforces our mental-state, and a feedback loop of either positive or negative processes becomes established. Research studies have shown beneficial effects of using brainwave entrainment for treating migraine headaches, premenstrual syndrome, and for managing physical pain.
The thing about conditioning is, it doesn’t matter whether the conditioned response is pleasant or unpleasant, desirable or undesirable. The process of conditioning works just as well both ways. You went looking for any indication you were getting an effect by using entrainment and you happened to have an unpleasant experience that you focused on. To the mind it is irrelevant whether it was pleasant or unpleasant. One way works just as well as the other. But the fact remains; it was your general expectations that resulted in a specific situation of conditioning.
Binaural meditation music is VERY popular these days, and you might have noticed that some of the companies that sell binaural music products make rather spectacular claims about the benefits of brainwave entrainment technology. Some declare that they can make you “meditate like a zen monk at the touch of a button”, or that you will “instantly meditate like the greatest gurus”. While it is true that binaural meditation music is extremely powerful, and that it can genuinely improve the quality of your life, it is not a miracle solution or a spiritual “get rich quick” scheme. Like all things in life, positive and lasting results will still take just a little time and effort on your part. Binaural meditation music just accelerates and deepens to process.

“One of the best ways to explain how brainwave entrainment works is by observing the effect of a tuning fork on a guitar string,” says Naik. “Hit a tuning fork tuned to a particular sound frequency, such as the note C, and hold it close to the strings of a guitar. You will notice that the C string on the guitar starts to vibrate because it has entrained on to the same frequency of the tuning fork.”

Entrainment is a term originally derived from complex systems theory, and denotes the way that two or more independent, autonomous oscillators with differing rhythms or frequencies, when situated in a context and at a proximity where they can interact for long enough, influence each other mutually, to a degree dependent on coupling force, such that they adjust until both oscillate with the same frequency. Examples include the mechanical entrainment or cyclic synchronization of two electric clothes dryers placed in close proximity, and the biological entrainment evident in the synchronized illumination of fireflies.[13]