Heller served as Assistant Professor of Economics (1965–68) and Associate Professor of Economics (1968–71) at UCLA. In 1971-1974 he was Professor of Economics at the University of Hawaii and served as Chairman of the Department in 1973-74. From 1974 to 1978 he was Chief of the Financial Studies Division of the Research Department of the International Monetary Fund in Washington D.C., where he was in charge of the IMF's monetary and financial research program. In 1978 he joined Bank of America in San Francisco as Senior Vice President and Director of International Economic Research . At Bank of America he was a member of the Management Advisory Council, the International Money Policy Committee, the Trust and Investment Policy Committee, the International Banking Council and the Policy Research Council. He also was Chairman of both the Foreign Exchange Outlook Committee and the Country Risk Rating Committee.
President Reagan nominated Heller in 1986 as a Member of the Board of Governors of the Federal Reserve System and he was confirmed unanimously by the U.S. Senate
At the Federal Reserve he served as the Administrative Governor and the Chairman of the Committee on Bank Supervision and Regulation. He was a member of the Federal Financial Institutions Examination Council and a Federal Reserve delegate to the Organization for Economic Co-Operation and Development in Paris. As the Administrative Governor he was responsible for the creation of the official flag of the Federal Reserve, which he designed with the help of his daughter Kimberly Allison.
At the Federal Reserve he championed giving investment banking powers to commercial banks, allowing U.S. banks to accept foreign currency deposits and the elimination of interstate banking barriers. He joined VISA International in 1989 as Executive Vice President in charge of global finance, audit and risk management. In 1991 he was appointed President and CEO of VISA U.S.A.. Heller was honored by the American Banker as a "Leader of the Bankcard Business"