While in college, Maher also played as an amateur with the Ocean City Barons of the Premier Development League (PDL). He spent three seasons with the Barons and in the 2004 Lamar Hunt U.S. Open Cup, the Barons played against the Syracuse Salty Dogs. At the time, his brother Anthony Maher was with the Salty Dogs. In the spring of 2007, Miami FC picked Maher in the first round (ninth overall) of the USL College Draft. Maher elected to finish his degree which caused him to miss the 2007 USL pre-season. Following graduation from Temple, Maher moved to Cary, North Carolina to live with his brother, Anthony, who was now playing with the Carolina RailHawks. Maher trained with the RailHawks, eventually gaining a contract offer mid-season. Maher made his first professional start against Liga MX México Primera División side Cruz Azul. In 2007, the New Jersey Ironmen of Major Indoor Soccer League (MISL) drafted Maher with the second pick of the MISL College Draft. During the 2007–2008 season, he was a Defensive Player of the Week, making him the first rookie to earn POTW honors. He scored his first career MISL goal on January 5, 2008 vs. Detroit Ignition. On January 7, 2009, he signed a contract with the Philadelphia KiXX of the newly formed NISL. At the time, his brother, Anthony Maher, also played for the KiXX. On March 1, 2009, Maher blew out his knee.