Mitsunari's defeat in the battle of Sekigahara is generally considered to be the beginning point of the Tokugawa shogunate, which ruled Japan for another two and a half centuries until 1868.

[9][10] In the years following the Imjin War and the death of Hideyoshi, factional disputes arose between Ishida Mitsunari and seven former Toyotomi generals including Katō Kiyomasa.

Tokugawa Ieyasu gathered both Kiyomasa and Fukushima Masanori to his cause in a bid to challenge the opposition from Mitsunari, who claimed to fight on behalf of the Toyotomi clan.

[12] Mitsunari met with Ōtani Yoshitsugu, Mashita Nagamori and Ankokuji Ekei, conspiring to raise an anti-Tokugawa army, of which Mōri Terumoto was appointed to be the overall commander.

Ōta Gyūichi, who was present at the battle, wrote in his chronicle that "friends and foes are pushing each other" and "gunfire thunders while hails of arrows fly in the sky".

[50][51] The Shimazu troops only managed to break their encirclement after devastating casualties, escaping with only 200 soldiers remaining; even then, they were pursued by Ii Naomasa until the latter was incapacitated by a shot from a rifleman.

[28] The combined Eastern Army forces of Tokugawa Hidetada and Sakakibara Yasumasa, who commanded as many as 38,000 soldiers, were at the time of the battle bogged down in the Siege of Ueda against Sanada Masayuki.

[55] Another Western Army contingent that failed to reach the Sekigahara battlefield was led by Tachibana Muneshige, who had been stalled by Kyōgoku Takatsugu in the Siege of Ōtsu.

[59] The most prominent political effect of the Eastern Army victory in Sekigahara was the shifting authority to assign military ranks[60] and redistribute lands from the Toyotomi clan to Tokugawa Ieyasu.

[61] Immediately following the battle, Ieyasu redistributed domains worth 6.8 million koku,[62] primarily as recompense for the allies instrumental in his victory:[63][64] Notably, Kobayakawa Hideaki, whose defection from the Western Army contributed greatly to Ieyasu's victory, was bestowed a domain which covered parts of Bizen Province and Mimasaka Province and which was worth 520,000 koku.

[68] Perhaps surprisingly, Ieyasu bestowed only meager domain increases to the three remaining Shitennō (Ii Naomasa, Honda Tadakatsu, and Sakakibara Yasumasa), his closest high-ranking generals, as compared to those he offered to newer commanders and vassals.

[70][71][72] As for the generals of the defeated Western Army, roughly 87 daimyō had their domains confiscated and their power stripped due to their support of Mitsunari in the battle.

[74] Suzuki Hyōe, vassal of Naomasa, relieved Kazutoyo with an army transported by 8 ships, ultimately pacifying the region in 5 weeks after killing about 273 enemies.

[75][76] On September 17, Ieyasu dispatched his army, led by Kobayakawa Hideaki, to attack Sawayama Castle in Ōmi Province, the home base of Mitsunari.

[77][f] In response to Shimazu Yoshihiro's support of the Western Army, Ieyasu prepared a massive punitive expedition to Kyushu, to be led by his son Tokugawa Hidetada.

In 1603, Ieyasu was officially appointed as shōgun by Emperor Go-Yōzei;[82][81][9] as such, the conclusion of the Battle of Sekigahara has served as the de facto beginning of the Edo period, and more generally, of the return of stability to Japan.

In 1664, Hayashi Gahō, Tokugawa historian and rector of Yushima Seidō, wrote: Evil-doers and bandits were vanquished and the entire realm submitted to Lord Ieyasu, praising the establishment of peace and extolling his martial virtue.