Naomasa's father, Ii Naochika, was falsely convicted of treason by Yoshimoto's paranoid successor, Imagawa Ujizane, and was subsequently killed.

Furthermore, he was granted possession of Iinoya in Shizuoka, former territory of Ii clan, and was appointed as a page of Tokugawa Ieyasu after visiting him in Hamamatsu Castle.

[11] At the age of 18, Naomasa participated in the Tokugawa army attack on Tanaka castle which guarded by Takeda clan general named Ichijō Nobutatsu.

In this battle, Naomasa fought together with Matsudaira Ietada, Sakakibara Yasumasa, and Honda Tadakatsu as they all climbed to Tanaka castle wall and fighting Nobutatsu's soldiers.

However, the Hōjō clan in the Kantō region also led an army of 55,000 men and crossed the Usui Pass to invade Shinano Province.

[30] Aside from military service, Naomasa played diplomatic role during this conflict as he received around 41 letters from many former Takeda clan's vassals to submit to Ieyasu.

[35] The result of this war, combined with the defection of Sanada Masayuki to the Tokugawa side has forced the Hōjō clan to negotiate truce with Ieyasu.

The soldiers were led by Tadatsugu, While Naomasa, Ishikawa Kazumasa, Honda Tadakatsu, Sakakibara Yasumasa, and Matsudaira Ietada were deployed in reserve before entering the battle with Ieyasu himself.

[f] In 1587, during the campaign of Toyotomi Hideyoshi against the Ikkō-ikki rebel armies, the Tokugawa clan were involved in the battle of Tanaka castle in Fujieda, Shizuoka.

The siege of Odawara, as the last Hōjō clan stronghold, nearly saw no significant military action, with the exception of Naomasa's night raid attack.

This happened after a group of miners from Kai Province dug under the castle walls, allowing men under Ii Naomasa's command to enter and engage the enemy.

[66] Later in October 28 of the same year, a massive rebellion against the Toyotomi government in Mutsu Province which was incited by Hienuki Hirotada and Waga Yoshitada broke out.

In response, Hideyoshi sent a punitive expedition with 30,000 army in strength led by Ieyasu Tokugawa, Toyotomi Hidetsugu, Date Masamune, Ishida Mitsunari, Ōtani Yoshitsugu, Gamō Ujisato, Uesugi Kagekatsu, Satake Yoshishige, and Maeda Toshiie, in order to pacify those rebellions.

This caused the punitive expedition army to take the measure of splitting their forces as Ieyasu, Naomasa, Ujisato, and some commanders now changed their focus to suppress Masazane's rebellion first.

[71] As the operation commenced, Naomasa became part of the army who besieged Kunohe castle, where he and Asano Nagamasa deployed on the east side across the Nekobuchi River.

[73][68][67] After the Kunohe clan was suppressed, Naomasa's detachment then rejoined the main expedition army with Mitsunari, Asano Nagamasa, and others to finish the operation to pacify the Hienuki and Waga clans, as Naomasa marched across Mutsu and Dewa Province subduing the resistances and capturing castles from Waga and Hienuki's allies during his journey.

The rebellions were finally suppressed by June 20th with Waga Yoshitada being slain in battle,[74] while Hienuki Hirotada was sentenced to "Kaieki law" which stated that he and his clan's status and rights as samurai were stripped.

[78] In 1600, on the eve of the Sekigahara campaign, Naomasa led the forces in the Tokaido area together with Honda Tadakatsu, and played a central role as Ieyasu's representative.

[79] The troops of Naomasa were reinforced with a detachment of Kugai Masatoshiwho was a vassal of Tokugawa Hidetada who was himself at that moment still busy in the Siege of Ueda castle.

[83] The first group led by Terumasa crossed the Kiso River and engaged in a battle at Yoneno, causing the Hidenobu army to be routed.

In this battle, Hidenobu's castle was deprived of the expected support from Ishikawa Sadakiyo (石川貞清), who decided to not help the Western army in this war after he made an agreement with Naomasa.

Hidenobu was prepared to commit seppuku, but was persuaded by Ikeda Terumasa and others to surrender to the eastern forces, and the Gifu Castle fell.

[87] However, some modern historians now view Naomasa's actions as a result of confusion on both sides as there was heavy fog covering the battlefield, and this may have caused him to unintentionally start the first clash against the enemy, which broke Ieyasu's previous order to let Masanori perform the first move of the battle.

[79][102][103] Several months after the battle in Sekigahara, Naomasa sent military reinforcements to assist Yamauchi Kazutoyo in pacifying the rebellion in Tosa Domain against retainers of Chōsokabe clan, and the Ichiryo Gusoku peasant army.

[3] Naomasa sent his vassal, Suzuki Hyōe, with force as strong as 8 ships to help Kazutoyo, which finally pacified the area in 5 weeks, after killing about 273 enemies.

[108] The "Clan records" chronicles from Edo period also stated that during the battle of Komaki-Nagakute, Naomasa were described as "handsome and has small physical stature".

[116][7] Historian Toshikazu Komiyama believed this steps were an effort of Ieyasu to strengthen and rejuvenate the Ii clan after facing danger of extinction due to decades of troubles which weakened them internally.

[127] Recently in 2023, a letter of Naomasa Ii's which was sent to a former Takeda general named Obata Nobusada (小幡信真)[j] during the conflict between Tokugawa against Hojo clan, was disclosed by Hiroko Noda, an official of Hikone castle museum.

[129] The warriors which Naomasa commanded on the battlefield were notable for being outfitted almost completely in blood-red armour from their mounted samurai, bannermen, to even ashigaru.

[8] The Iinoya trio were a powerful clans that originated from eastern side of Mikawa who contributed much for Ieyasu expansion during his conquest of former Imagawa territories in Tōtōmi Province.