Naeher attended Penn State from 2006–2009. She started 74 games during that span with a record of 50–19–5 with 24 shutouts. She was a First Team All-American in 2007 and 2008 and was named the Big 10 Defensive Player of the Year in 2007.
She started her career with the Women's National Team in 2008 when she played in the U-20 World Cup only conceeding one goal and earning herself the Golden Glove award. Naeher made her first appearance with the USWNT in 2014 with her first career shutout at the highest level. She made the roster for the 2015 World Cup and 2016 Summer Olympics as the backup to goalkeeping legend Hope Solo. In the 2019 World Cup, Naeher was named the team's starting goalkeeper. She was the goalie for the 2020 Olympic Bronze Medal winning team.
Naeher has played for the Boston Breakers and Chicago Red Stars in the NWSL.