End grain will always stain darker than the rest of the piece because end grain absorbs more of a pigmented stain. An easy way to avoid this is to mix a 50:50 solution of your desired stain color and the same manufacturer’s ‘natural’ or ‘clear’ stain. Apply this diluted stain to end grain and it will appear the same color as undiluted stain applied to the rest of the piece. NOTE: It is extremely important to use the same manufacturer for both stains, or you will risk ingredient incompatibility which will cause curing problems. Manufacturers do not list ingredients, but unless a particular manufacturer suddenly changes their recipes, it is unlikely you will have ingredient incompatibility problems if you use a single brand.
Another easy way is to use a gel stain; but these stains are more expensive. There are fewer color choices available, and it is more difficult to consistently mix stains to obtain a customized color.
– Steve Hendrickson