After the death of his father, Suleiman ibn Kutalmish, in 1086, he became a hostage of Sultan Malik Shah I, but was released when Malik Shah died in 1092. Kilij Arslan then took over the Seljuk army and set up his capital at Nicaea, killing his own father-in-law Emir Chaka of Smyrna in order to stabilize the Sultanate. He also invaded the Danishmend Emirate of Malik Ghazi in eastern Anatolia, although the two allied with each other in 1096 when the peasant Crusader army of Peter the Hermit and Walter the Penniless arrived at Nicaea. His army easily defeated the mob. About 20 000 Crusaders were killed and the rest were sold into slavery.
Because of this easy victory he did not consider the main Crusader army, led by various nobles of western Europe, to be a serious threat. He resumed his war with the Danishmends, and was away from Nicaea when these new Crusaders attacked Nicaea in May of 1097. He hurried back to his capital to find it surrounded by the Crusaders, and was defeated in battle with them on May 21. The city then surrendered to the Byzantines.
As the Crusaders continued their march across Anatolia, Kilij Arslan planned an ambush near Dorylaeum on June 29. However, his archers could not penetrate the line of defense set up by the Crusader knights, and a separate group of knights was able to capture the Turkish camp. Kilij Arslan retreated, and did not attack the Crusaders again, although he destroyed crops and water supplies along their route.
In 1101 he defeated another Crusader army at Heraclia, which had come to assist the fledging Crusader States in Syria. This was an important victory for the Turks, as it proved that an army of Crusader knights were not invincible. After this victory he moved his capital to Konya.
In 1104 he resumed once more his war with the Danishmends, who were now weakened after the death of Malik Ghazi. In 1107 he conquered Mosul, but he was defeated by Ridwan of Aleppo. While retreating from Mosul he drowned in the Habura river.