When she was young, Konan's family was killed during the Second Shinobi World War, and she was left to fend for herself.[2] Some time later, Yahiko found her, and the two worked together to survive. Not long after that, Konan went for a walk and found a young, dying Nagato and his dog, Chibi. She then rescued him and brought him back to their hideout. Gradually the three became very close friends. They eventually encountered the Sannin, who gave them some food. Konan impressed them by making an elaborate flower out of the paper wrappers left behind as a sign of gratitude. When Orochimaru suggested to kill them so they would not have to suffer the horrors of war, Jiraiya instead opted to stay and teach the three how to look after themselves.
 
        After Jiraiya taught them ninjutsu and was confident they could take care of themselves, he left them on their own. Before leaving Jiraiya tells Konan that she will be very beautiful when she grows up and to come and see him when she turns eighteen.[3] During their time with Jiraiya, he made a defence system (seeing as that the hideout they all shared at the time was vulnerable to being targeted for enemy attacks) composed of four planks, each with one red side and one white (the white side also had a frog picture on it), attached to a part of a wall of the hideout they shared at the time with a string and a nail, each one above one of their names, which he called "Hop-In" planks. Nagato's, Yahiko's and Konan's were one wall and Jiraiya's was on a wall opposite. The purpose of the planks were that when they were in the hideout, they turn their planks to the red side and they leave, they flip their plank to the white side, so when a plank's on the red side and the person's not in the hideout, it means they could have been captured by the enemy and when a plank's on the white side and it appears that the person's in the hideout, it could mean that an enemy has transformed into said person and has infiltrated the hideout, along with a trapdoor hidden among the floorboards leading to an hidden room and emergency escape route he left just in case.

        As they fought, Jiraiya countered her paper techniques with an oil-based attack and immobilised her with his elongated hair, but she was saved when Pain appeared to wash the oil away.