Early modern travellers such as Buondelmonti (1415), Basilicata (1630) and Tournefort (1700) visited the hill of Aptera and recorded their impressions. In 1834, Pashley was the first to correctly identify the site as that of the ancient city.

In 1862 and 1864, the French School of Archaeology at Athens conducted the first excavations at Aptera, which brought to light the ‘wall of inscriptions’, a large structure with honorary and proxeny inscriptions of the 3rd and 2nd centuries BC. In 1942, the German forces of occupation excavated the small two-room temple.

The Archaeological Service began (mostly rescue) excavations in 1958, later continued by the 23rd Ephorate of Prehistoric and Classical Antiquities. Systematic excavations in the city centre began in 1985−1987 and continue to this day. Rescue excavations are also continuing in the areas surrounding the archaeological site.

The investigation, protection, and promotion of the archaeological site have greatly benefitted from funding by Regional European Programmes. Extensive conservation and rescue interventions to the masonry of the cisterns and baths were carried out in 1999–2000 (Second Community Support Framework), followed by conservation of the fortifications in 2003−2006 (Third Community Support Framework), and of the main gate in 2010−2012 (National Strategic Reference Framework). The ancient theatre was excavated and restored in 2008−2015 (National Strategic Reference Framework). Systematic excavations continue in the Roman House and the ‘Temple of Dionysus’ with annual funding provided by the Region of Crete.