McCarthy moved back to the National League to play for the Boston Beaneaters in and enjoyed his most productive seasons over the next few years. In he drove in over 100 runs for the first time in his career, a feat that he repeated in while hitting 13 home runs. The press of the day called McCarthy and teammate Hugh Duffy the "Heavenly Twins". Their Boston team was one of the most successful clubs of the era. McCarthy played for the Brooklyn Bridegrooms in before retiring. He finished his career with a .292 batting average, 44 home runs and roughly 500 stolen bases.