The museum houses Greek works of art from the prehistorical to the modern times, an extensive collection of Asian art, hosts periodic exhibitions and maintains a state-of-the-art restoration and conservation workshop.

Although the museum initially housed a collection that included Islamic art, Chinese porcelain and exhibits on toys, it's 2000 re-opening led to the creation of satellite museums that focused on specific collections, allowing the main museum to focus on Greek culture over the span of the country's history.

The Benaki Museum was established in 1930 by Antonis Benakis, a Greek entrepreneur, in memory of his father, Emmanuel Benakis. It is one of the most important museums in Greece and its collection includes over 45,000 artifacts from various historical periods and cultures from across the world. Its main collection includes prehistoric, Egyptian, Byzantine, and post-Byzantine artifacts, as well as a wide range of modern and contemporary art. The Benaki Museum is divided into eight sections, each focusing on a period or a culture.

These sections include the Ancient Greek, Byzantine and Islamic Art, the Benaki Collection of Islamic Art, the Greek Folk Art Collection, the Chinese and Japanese Art Collection, the Indian and Himalayan Art Collection, the European Art Collection, the Contemporary Greek Art Collection, and the Greek Costume Collection. The museum is also home to a library and a research center. The library consists of over 35,000 volumes and is a valuable resource for scholars of Greek and world culture. The research center houses an extensive archive of photographs, documents, and manuscripts related to the history of Greece and the Mediterranean region. The Benaki Museum also hosts a variety of educational and cultural activities, including lectures, seminars, and exhibitions.