Niese was born to Jeffery and Annette Niese in Lima, Ohio, on October 27, 1986, the same day that the Mets won their second World Series. He was brought up in Defiance, Ohio where he attended Defiance High School. He played soccer all four years of high school and was named Third Team All-State during his junior year. In 2004 and 2005, he was named the state's baseball Player of the Year, becoming the first athlete to win the award in consecutive seasons. In Little League (and later in high school), Niese was a teammate of Major League pitcher Chad Billingsley. In the 2005 Major League Baseball Draft, the Mets chose Niese 209th overall (ninth pick of the seventh round).