The ship was sent to the Far East almost immediately after entering service in 1899, where she participated in the suppression of the Boxer Rebellion the next year and was the flagship of the First Pacific Squadron.

At the beginning of the Russo-Japanese War of 1904–1905, Petropavlovsk took part in the Battle of Port Arthur, where she was lightly damaged by Japanese shells and failed to score any hits in return.

Casualties numbered 27 officers and 652 enlisted men, including Vice Admiral Stepan Makarov, the commander of the squadron, and the war artist Vasily Vereshchagin.

Petropavlovsk departed Kronstadt on 17 October and arrived at Port Arthur on 10 May 1900, becoming the flagship of Vice Admiral Nikolai Skrydlov and the First Pacific Squadron.

[9] As tensions with Japan increased, the Pacific Squadron began mooring in the outer harbor at night in order to react more quickly to any Japanese attempt to land troops in Korea.

Petropavlovsk was not hit and sortied the following morning when the Japanese Combined Fleet, commanded by Vice Admiral Tōgō Heihachirō, attacked.

[14] As a result of the damage incurred in the attack by the more heavily armored Tsesarevich and the subsequent lengthy repair time, Makarov was compelled to retain Petropavlovsk as his flagship, against his better judgement.

[12][13] Having failed to blockade or bottle up the Russian squadron at Port Arthur by sinking blockships in the harbor's channel,[16] Tōgō formulated a new plan.

Covered by four detachments of torpedo boat destroyers, the minelayer Koru-Maru began to lay a minefield near the entrance to Port Arthur on the night of 31 March.

Once her captain realized his mistake, the Russian ship attempted to escape but failed after a Japanese shell struck one of her torpedoes and caused it to detonate.

Escorted by three protected cruisers, Makarov led Petropavlovsk and her sister Poltava out to support Bayan, while ordering the rest of the First Pacific Squadron to follow as soon as they could.

[18] After the squadron had united and turned back towards the enemy, about two nautical miles (3.7 km; 2.3 mi) from the shore, Petropavlovsk struck one or more mines at 09:42 and sank almost instantly,[19] taking with her 27 officers and 652 enlisted men, including Makarov and the war artist Vasily Vereshchagin.

[22][23][24] A monument was constructed in Saint Petersburg in 1913 to honor Makarov after Japanese divers identified his remains inside the wreck of Petropavlovsk and gave him a burial at sea.