He also has the highest career earnings in MLB history. The highest paid player in Major League Baseball (MLB) from the 2013 season is New York Yankees ' third baseman Alex Rodriguez with an annual salary of $29,000,000, $4 million higher than the second-highest paid player, Cliff Lee.e also has the highest career earnings in MLB history. The highest paid player in Major League Baseball (MLB) from the 2013 season is New York Yankees ' third baseman Alex Rodriguez with an annual salary of $29,000,000, $4 million higher than the second-highest paid player, Cliff Lee.