From 1842 to 1846, Frederick Charles was under the military tutelage of then major Albrecht von Roon, who accompanied the Prince to the University of Bonn in 1846. After his studies, the Prince served as a captain on Wrangel's staff during the Schleswig campaign of 1848. Promoted to major on the general staff, he partook in a campaign in Baden during which he was wounded. During the following peace years he was promoted to colonel in 1852, major general in 1854 and lieutenant general in 1856. In 1860, the Prince published a military book, titled, "Eine militärische Denkschrift von P. F. K.". Promoted to General der Kavallerie, the Prince took part in the Second Schleswig War of 1864 against Denmark, where he held command over the Prussian troops in the Austro-Prussian expeditionary force but interfered in the plans of his chief of staff, von Blumenthal, who turned to Crown Prince Frederick William for support.
He served with distinction in the Austro-Prussian War, where he commanded the First Army; consisting of 2nd, 3rd and 4th corps. Arriving first at Königgrätz, he held the numerically superior Austrians at bay until his cousin the Crown Prince (who now had General von Blumenthal as his Chief of Staff) and his Second army came up and attacked the Austrians in the flank.