Eczacıbaşı joined the Eczacıbaşı Pharmaceutical Company in 1955 and from 1956 to 1967 published the journal Tıpta Yenilikler (Innovations in Medicine), which deeply affected the milieu of arts and culture as well as the medical community. Moreover, he organised Eczacıbaşı Cultural Films series together with Sabahattin Eyuboğlu and Pierre Biro between 1960 and 1962. One of the films among the series, Renk Duvarları (Walls of Colour), won the Council of Europe Cultural Film Award in 1964.
In 1965, together with Onat Kutlar, he leaded the foundation of the Turkish Cinemateque Foundation, which he headed for ten years.
In his business career, Şakir Eczacıbaşı became the general manager of Eczacıbaşı Pharmaceuticals in 1970s, chairman of the Executive Committee of the Eczacıbaşı Group on 1980, and the Chairman of Eczacıbaşı Holding in 1993.
The basketball, volleyball, and table tennis teams that he established in 1966 won numerous championships in Turkey. Şakir Eczacıbaşı continued to head the Eczacıbaşı Sports Club until 1996. The club represented Turkey in a number of European cups for years.
One of the most famous modern photographers of Turkey, Şakir Eczacıbaşı's encounter with photography goes back to 1960s. His photographs were exhibited in 15 exhibitions in Turkey and in 25 exhibitions abroad. Some of his works were published in the books titled Anlar/Moments (1983), Türkiye Renkleri (Colors of Turkey) (1997), Kapılar ve Pencereler (Doors and Windows) (2001) and Bir Seçki (A Selection): 1965-2005 (2005).
From 1968 onwards he published the "Eczacıbaşı Colour Photograph Almanacs" with contributions from prestigious authors and photographers. These publications also served to introduce many unknown young talents. He was also the editor of two books, one a collection from Bernard Shaw, titled Gülen Düşünceler (Laughing Thoughts) and the other from Oscar Wilde titled Tutkular, Acılar, Gülümseyen Deyişler (Passions, Pains, and Smiling Parables). He was also among the pioneers of the foundation of Milliyet Sanat, a prominent journal of Turkish arts world, upon the request of Abdi İpekçi in 1972.
He was awarded with the Medal of Art and Education Cavalier by France and with the Medal of Eminent Service by Turkey. He ceased his activities in the business world in 1996 and focused on İstanbul Foundation for Culture and Arts (İKSV), of which he became the chairman in 1993. Throughout the 16 years that he headed the establishment, İKSV, which began its activities with a single festival of one and a half months, grew to be a foundation with outmost importance for the cultural and artistic life of Turkey, organising five different festivals on international scale. The Film Days that grew to be the International İstanbul Film Festival, one of the most important film festivals of Europe, thanks to the efforts of Şakir Eczacıbaşı. Eczacıbaşı has also contributed to the intellectual life in Turkey with his efforts for uncensored screening of festival films, since 1988. Şakir Eczacıbaşı has also contributed greatly to the continuance of International İstanbul Theatre Festival, which has gained international eminence despite limited resources.
Şakir Eczacıbaşı had always believed that a well-organized and fruitful "cultural life" should be formed in Turkey. For this purpose, in addition to his efforts with İKSV he formed the Culture Initiative along with leading figures of Turkish cultural life. The Culture Initiative has realised seven important cultural symposia since 1998. İKSV has published the valuable volumes that compile the discussions that took place at these symposiums.
Şakir Eczacıbaşı has also initiated İKSV Design, an establishment that produces exclusive and limited souvenir material that brings together art and design. In the past four years, he personally took interest in every small detail from designs to the artists chosen to be invited to contribute to the collection.
Şakir Eczacıbaşı has accomplished the aspiration of Dr. Nejat F. Eczacıbaşı, one of the founders of the Foundation, by realising the dream of İKSV to move to its own building. İKSV's new building will become a permanent part of İstanbul's cultural and artistic life, and will thus realise the dream of Şakir Eczacıbaşı.
Şakir Eczacıbaşı has recently authored a book of his memoirs, Çağrşımlar, Tanıklıklar, Dostluklar, which is published in 2010 by Remzi Kitabevi.