We examine the long-term variability of the near-surface circulation of the Ionian Sea. Our analysis primarily focuses on a high-resolution hindcast simulation of the Mediterranean dynamics from 1981 to 2010. This time period is significant as it includes a notable near-surface circulation reversal in the Northern Ionian Sea (NIS), which shifted from anticyclonic to cyclonic at the end of 1997. This transition has been previously documented by altimeter data and Copernicus reanalysis. Our hindcast simulation accurately captures this change. Here we examine the temporal and spatial scales of the near-surface circulation during the transition and investigate the factors contributing to the observed variability of the basin dynamics, including local wind-stress, deep-water density anomalies, and the lateral current associated with the Atlantic Ionian Stream (AIS). We find that while wind stress does play a role, the primary factor driving long-term variability in the NIS near-surface circulation is the AIS. During the late 1980s to mid-1990s, the AIS was weak and local cyclonic winds were also weak, allowing the AIS to enter the NIS along the coasts of Sicily. This led to the formation of a wide anticyclonic cell in the NIS. From the mid-1990s to 2010, the AIS was stronger and, favored by stronger cyclonic winds, detached from the coasts of Sicily heading directly towards the Levantine basin without penetrating the NIS. This process led to the formation of a wide cyclonic cell over the NIS. These results highlight the role of the AIS in controlling the circulation of the NIS.