Moglia spent 17 years at Merrill Lynch, where he was a member of the executive committees for both the institutional business and the private client business. Before leaving to take the role of chief executive officer at Ameritrade Holding Corp in 2001, he was responsible for all investment products, the insurance company, the 401 business and the middle-market business. In his seven years at TD Ameritrade, Moglia and his executive management team oversaw the company as its client assets grew from $24 billion to over $300 billion, increased its market capitalization from $700 million to $12 billion and produced five consecutive years of record earnings performance. He has also helped the company capitalize on merger and acquisition opportunities, including two of the largest in the discount brokerage industry: Datek Online Holdings in September 2002 and TD Waterhouse in January 2006. In March 2008, citing the desire to pursue other interests, Moglia announced he would be vacating the CEO position in the coming fall. A search for his successor took place over the spring and summer. In September 2008, Moglia officially stepped down from his CEO position at TD Ameritrade. Fred Tomczyk, the former COO at TD Bank Financial Group, succeeded him. Not completely leaving the company, Moglia became the new chairman, succeeding J. Joseph Ricketts. It was the first time in the company's history where no member of the Ricketts family was a member of the management team, outside of the few that remain as independent directors on the board of directors.
Return to coaching
After stepping down as CEO, Moglia began work for the University of Nebraska as executive advisor to the head football coach under Bo Pelini. On November 10, 2010, Moglia was named as the head coach of the new United Football League franchise, the Virginia Destroyers. On January 12, 2011, he was then named President and head coach of the Omaha Nighthawks, whose venue was TD Ameritrade Park Omaha. As the UFL's financial position deteriorated, Moglia signed with Coastal Carolina on December 20, 2011, replacing David Bennett. In his first season with Coastal, he led the team to win the 2012 Big South Conference Championship and was named 2012 Big South Conference Coach of the Year. After the 2015 Big South season, the Chanticleers program began the transition to FBS, the highest level of college competition. Coastal Carolina joined the Sun Belt Conference for non-football sports in July 2016, and became Sun Belt football members in 2017, the second and final year of the FBS transition. They were not eligible for bowl games or the Sun Belt football title during this period. On July 28, 2017, Moglia went on medical leave; the school announced on January 5, 2018 that he had been medically cleared to return to full-time coaching. Jamey Chadwell, whom Moglia had hired as his new offensive coordinator in January 2017, served as Coastal's interim head coach during Moglia's leave.
Retirement from coaching
On January 18, 2019, Moglia announced that he would be stepping down as head coach of the Coastal Carolina Chanticleers football team and turn the head coach position over to Jamey Chadwell, who served as his offensive coordinator and as interim coach during his leave of absence. Moglia stated that even though his contract runs until 2021, he believed that it was in the best interest of the program to do so.