In his youth, he moved to Tanzania, where his father worked as a geologist. From 1969 to 1970, he studied at a high school in Tanzania. Later he continued his studies at the Mining Technical School in Příbram (1970–1974). In 1979 he graduated in geology from the Charles University in Prague. Since 1980, he works in Geologic Institute of Czech Academy of Sciences and specializes on geology of Cenozoic Era. He also explores interactions between environment and civilization. Between 2004 to 2012, he was the director of the Geologic Institute of Czech Academy of Science.
In 2004, Cílek was awarded Tom Stoppard Prize for his books Krajiny vnitřní a vnější (2002) and Makom: Kniha míst (2004). Additionally, he was named Laureate by the Minister of Ecology for "valuable contribution to the popularization of Czech science, especially geology and climatology" (2007). In 2009, he was awarded the Václav Havel FoundationVIZE 97 Prize.