Her keel was laid in October 1861 at the Stabilimento Tecnico Triestino shipyard; she was launched in June 1862, and was completed in March 1863.

She carried her main battery—composed of sixteen 48-pounder guns and fifteen 24-pounders—in a traditional broadside arrangement, protected by an armored belt that was 110 mm (4.3 in) thick.

After the war, Prinz Eugen was modernized slightly in 1867 to correct her poor seakeeping and improve her armament, but she was nevertheless rapidly outpaced by naval developments in the 1860s and 1870s.

[2] During the Second Schleswig War in 1864, Prinz Eugen and the two Drache-class ironclads remained in the Adriatic to protect Austria's coastline while a squadron was sent to the North Sea to attack Denmark.

[4] Persano then spent the next two days bombarding the Austrian defenses of the island and unsuccessfully attempting to force a landing.

Tegetthoff received a series of telegrams between the 17 and 19 July notifying him of the Italian attack, which he initially believed to be a feint to draw the Austrian fleet away from its main bases at Pola and Venice.

Affondatore passed close to Prinz Eugen but failed to ram her or score any hits on the Austrian vessel.

[9] By this time, Re d'Italia had been rammed and sunk and the coastal defense ship Palestro was burning badly, soon to be destroyed by a magazine explosion.

Persano broke off the engagement, and though his ships still outnumbered the Austrians, he refused to counter-attack with his badly demoralized forces.

The Italian ships never came, and on 12 August, the two countries signed the Armistice of Cormons; this ended the fighting and led to the Treaty of Vienna.

[12] The fleet embarked on a modest modernization program after the war, primarily focused on re-arming the ironclads with new rifled guns.

Reconstruction projects were routinely approved by the parliament, so the navy officially "rebuilt" Prinz Eugen and her sister ships.