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In February 1943 the division was moved back to the Eastern Front as part of Erich von Manstein's Army Group South. The division, as a part of Paul Hausser's Panzer Corps, took part in the Third Battle of Kharkov, blunting the Soviet offensive.

During this campaign, Theodor Eicke was killed when his spotter aircraft was shot down. Hermann Priess succeeded Eicke as commander. The SS Panzer Corps, including the division, was then shifted north to take part in Operation Citadel, the offensive aimed at reducing the Kursk salient. It was during February 1943 that the 3rd SS Panzer Regiment received a company of Tiger I heavy tanks.

The attack was launched on 5 July 1943 with the II SS Panzer Corps attacking the southern flank of the salient as the spearhead for Generaloberst Hermann Hoth's 4th Panzer Army. The division covered the advance on the left flank of the II SS Panzer Corps, with the SS Division Leibstandarte forming the spearhead. With the advance slower than had been planned, Hausser ordered his II SS Panzer Corps to split in two, with the Totenkopf crossing the Psel River northwards and then continuing on towards the town of Prokhorovka. In the early morning of 9 July, 6th SS Motorised Regiment Theodor Eicke attacked northwards, crossing the Psel and attempted to seize the strategic Hill 226.6, but failed to do so until the afternoon. This meant that the northern advance slowed and the majority of the division was still south of the Psel, where elements of 5th SS Motorised Regiment 5 Thule continued to advance towards Prokhorovka and cover the flank of the Leibstandarte.

By 11 July, elements of the division crossed the Psel and secured Kliuchi. In the afternoon of 12 July, near the village of Andreyevka on the south bank of the Psel, the Soviet forces launched a major counterattack against Regiment Thule and the division's battalion of assault guns during the Battle of Prokhorovka.[11] Elements of the division engaged lead units of the 5th Guards Tank Army, halting the Soviet advance and inflicting severe damage to the Soviet forces, but at the cost of the majority of the division's remaining operational tanks. While the II SS Panzer Corps had halted the Soviet counteroffensive, it had exhausted itself. Citadel was called off on 14 July.

Along with the SS Division Das Reich, the division was reassigned to General Karl-Adolf Hollidt's reformed 6th Army in southern Ukraine. The 6th Army was tasked with eliminating the Soviet bridgehead over the Mius River. The division was involved in heavy fighting over the next several weeks. During the July–August battles for Hill 213 and the town of Stepanovka, the division suffered heavy losses, and over the course of the campaign on the Mius-Front, it suffered more casualties than it had during Operation Citadel. By the time the Soviet bridgehead was eliminated, the division had lost 1,500 troops; the Panzer regiment was reduced to 20 tanks.

Totenkopf was then moved north, back to Kharkov. Along with Das Reich, Totenkopf took part in the battles to halt Operation Rumyantsev and to prevent the Soviet capture of the city. The city was abandoned on 23 August due to the threats on the German flanks. In October 1943, the division was reformed as a Panzer division. The Panzer battalion was officially upgraded to a regiment, and the two motorised regiments were given the titles "Theodor Eicke" and "Totenkopf". The division, along with other Axis formations, continued its retreat towards the Romanian border. By November, Totenkopf was engaged in fighting against Red Army's attacks over the vital town of Krivoi Rog to the west of the Dniepr.