Egeskov Castle's builder, Frands Brockenhuus, did not make compromises in the construction of the castle. It is believed that Morten Bussert, master builder to King Christian III, served as the architect for the castle, which was completed in 1554.

It was a time characterized by the construction of residences as fortifications, serving both aesthetic and practical purposes by making it difficult for intruders to gain access. This was largely due to the political unrest and the recently concluded Danish Civil War, the Count’s Feud, in the 1530s. Frands Brockenhuus also took precautions by surrounding the castle with water on all sides.

After several years of construction, the castle was completed in 1554. It was built during a transitional period in styles within art and architecture, where one can perceive the sobriety of late Gothic and the order and symmetry of the Renaissance, as illustrated by the facade.

Egeskov Castle still stands today as one of Northern Europe's best-preserved water fortresses. The castle consists of a rectangular double house, which has origins in Dutch or Schleswig building styles. The structure rests on a driven pile foundation, likely supplemented with overhead, transverse oak logs, insulated with an upper layer of claystone and stone packings where the masonry is established. The voids between the logs were filled with stones, earth, and clay, which could also retain moisture. It remains crucial today that the timber foundation is below the water level to protect it from erosion. The current count's grandfather, Gregers, noted that there are as many as seven insulating layers in the foundation.

The two longhouses are connected by a meter-thick wall that contains both stairs and a well. This connection between the longhouses meant that in the event of an attack, one building could be abandoned while continuing the defense from the other. In the Knight's Hall, the massive wall is clearly visible. The outer walls were equipped with shooting slits and loopholes, which can still be clearly seen in the Stair Tower.

Between 1883 and 1884, the castle underwent a significant renewal to take on the form we know today. The gabled roofs were notably raised, as were the spires of the corner towers, which were now covered in copper. The Ladegårdsholmen was also cleared a few years earlier, allowing the gate wing to be constructed. The restoration was carried out under the direction of the Swedish architect, Helgo Zettervall. Today, Egeskov Castle is a listed building.