Sekler was born in Vienna to Eduard and Elisabeth Sekler, both of whom were actors. He studied architecture at the Technische Universität Wien (Vienna University of Technology), graduating with distinction in 1945, working as a practicing architect in the city beginning in 1946. He moved to London under a British Council Fellowship entering the School of Planning and Regional Research, London. In London, Sekler worked under Rudolf Wittkower Warburg Institute, Univeristy of London. Sekeler's wrote a dissertation on the evolution of the staircase in British architecture, granted by the Warburg in 1948. As a Fullbright Fellow, he travelled to the United States in 1953. In 1954 Josep Lluis Sert dean of the Graduate School of Design at Harvard, invited Sekler to lecture there. Sekler began lecturing at Harvard's design school in 1955 as a visiting professor, advancing to associate professor in 1956. His work led to the publication of Wren and his Place in European Architecture in 1956, the first serious attempt to explore the influences on that British architect. He married a Harvard graduate student in art history Mary Patricia May. At Harvard, Walter Gropius the previous head of the architecture department (Graduate School of Design between 1938 and 1952) being a vigorous Bauhaus modernist, had eliminated architectural history courses from the School. His successor, Josep Lluis Sert (1902-1983) appointed Sekler to counter that. In 1960, Sekler was made full professor at the architecture school. During these years, Sekler reversed the anti-historical the tradition of the School by eliminating courses and building an architectural-history library. He was assisted in this by another part-time faculty at the GSD--formerly full faculty at Harvard--Sigfried Giedion. Giedion's view of architectural history, however, was that all periods and styles were the road to the ultimate goal, modernism (Hoffman). Sekler, in his courses, took a more diverse view. As a lecturer, he instilled an enthusiasm for architectural history, including, for example, Cistercian architecture, kindling an enthusiasm in one student later to become an eminent Cistercian architectural historian, Peter J. Fergusson. In 1962, Sekler was appointed coordinator of studies at the newly-built Carpenter Center for the Visual Arts at Harvard. CCVA.
After visiting Kathmandu in 1962, Sekler joined efforts to preserve the cultural and architectural heritage of Nepal's Kathmandu Valley. He assisted UNESCO in plans to protect the valley's heritage from development. He combined his interest in architectural history and the work of his countryman, Josef Hoffmann in several works, beginning with one on the Stoclet Hous in 1967. He became director of the CCVA in 1968, overseeing the Le Corbusier-designed building, the only building designed by Le Corbusier in the United States. Sekler co-founded the Department of Visual and Environmental Studies (VES) with Albert Szabo.Sekler taught in proximity to Harvard's eminent historian of medieval architecture, Kenneth John Conant. When Sert, along with Albert Szabo founded the university's Visual and Environmental Studies department in 1968, Sekler was added to the faculty. He continued his interest in Nepal preservation, founding the Kathmandu Valley Preservation Trust in 1990. Sekler's primary appointment at Harvard remained in the Graduate School of Design, training practicing architects in architectural history. From 1970 onwards he was chosen to advise on many historic preservation projects in the United States and Austria. He founded the Kathmandu Valley Preservation Trust (KVPT) in 1990, serving as an honorary member of its board of directors. He retired as Osgood Hooker emeritus professor of visual art and emeritus professor of architecture. A festschrift edited by Alexander von Hoffman, Form, Modernism, and History: Essays in Honor of Eduard F. Sekler. He died at his home in Cambridge, Massachusetts.
His pioneering book, Wren and his Place in European Architecture, effectively explored the architect's continental sources (Summerson). He "devoted his professional career to securing a place for history in contemporary architecture." (Hoffman). In contrast to Conant's approach to medieval history at Harvard, "the form of Cistercian monasteries became clear through an examination of the daily functions of monastic life [for Sekler]" (Weese).