- Saki Watanabe: Saki is a childhood friend of Satoru and a fellow member of Group 1. Though they were often at odds, Saki has stated that their arguments were also a form of affection. They were among the last to graduate from Harmony School. Satoru has behaved very protectively of Saki throughout the series. During their capture by the Ground Spider colony, they had engaged in sexual intimacy, though not intercourse. When they escaped to the Robber Fly colony, Saki was able to restore his Cantus, which he used to attack the Ground Spiders with Saki acting as his back-up pair of eyes. After the first timeskip and Shun's death, the two formed a duty pair upon realizing that Ryou was not the one they both fell in love with. After Maria and Mamoru had left the village, Satoru acted as Saki's pillar of strength after she lost her best friend and lover. During the night in the snow hut while they were searching for Maria and Mamoru, the two had sex. The manga implies they had more intimate moments over the years. Immediately following the second timeskip, the two had fallen out over a petty argument and stopped talking for a month, but had reconciled easily when they met again. In the manga, Satoru even contemplated proposing to her. When the town came under attack by the Queerats and the Fiend and they encountered the mutated Queerat that spewed gunpowder, Saki and Satoru had used their Cantus to save each other rather than themselves. In Tokyo, Satoru chose to go with Kiroumaru when they had to split up, believing that Saki would be safer with Inui. He had also volunteered to carry the Psychobuster with the intention of sacrificing himself if the need arose. When he threw the Psychobuster at the Messiah after their plan failed, he knew that he would end up infected as well. However Saki burned the Psychobuster, as she couldn't bear the thought of losing her last remaining friend, and be the sole survivor of Group 1. At the end of the series, Satoru and Saki are married with a child on the way. Both were certain that by the time that their child was born, their society would be become much better.
- Shun Aonuma: Shun is a childhood friend of Satoru and a fellow member of Group 1. They were first seen playing capture-the-flag on the hill, whereupon Satoru expressed displeasure over Saki and Shun bonding over the minoshiro. Satoru initially treated Shun like a rival and constantly competed with him as a child, but developed feelings for Shun after the first timeskip and became his boyfriend. Shun had to be persuaded into entering a relationship, but seemed to reciprocate Satoru's feelings. However, Shun abruptly ended the relationship, stating that he was tired of being Satoru's doll and that he wanted to be by himself for a while, leaving Satoru heartbroken. However, when he suddenly disappeared from school, Satoru was still among the first to propose looking for him as it became obvious that Shun did not break up with him because he disliked him. When Saki found Shun at the bungalow, he revealed that he was turning into a Karma Demon, and that his leaking Cantus would eventually corrupt everything around him, and that keeping his distance from his friends would be the safest for them.
- Maria Akizuki: Maria is a childhood friend of Satoru and a fellow member of Group 1. They were first seen playing on the same side in the capture-the-flag game on the hill as children. The montage in Episode 16 showed Satoru, Maria, and Saki playing together as young children. After Maria and Mamoru's departure from the group, Satoru is shown to be saddened, albeit not as brokenhearted as Saki. When her death was confirmed by Tomiko Asahina at the Security Council meeting after the second timeskip, he is shown to be distraught, but to a lesser degree than Saki.
- Mamoru Itou: Mamoru was a fellow member of Group 1.
- Reiko Amano: Reiko is Satoru's childhood friend and a fellow member of Group 1. Satoru expressed irritation at Reiko's poor control of her Cantus that often caused Group 1 to come in last in class. When she was disposed of, he forgot about her.
- Squealer/Yakomaru: Squealer is a Queerat from the Robber Fly colony who rescued Saki and Satoru when they were escaping from the Ground Spider colony. He goaded Satoru into attacking the Ground Spiders and betrayed them several times before they parted. After the first timeskip, he used Saki and Satoru to threaten the Goat Moth colony into allying with the Robber Fly colony, under the pretense of helping them look for Maria and Mamoru. After the second timeskip, he attacked Kamisu 66 and pursued Satoru's group to Tokyo, where he was finally defeated and captured. Before his trial, Satoru met him and said that there was no point in reasoning with him. During the trial, Squealer shouted that they were humans, which prompted Satoru to look into Queerat DNA and discover that they were indeed mutated humans.
- Kiroumaru: Kiroumaru is a Queerat general of the Giant Hornet colony, which came to reinforce the Robber Fly troops in their war with the Ground Spider colony. Satoru saved his life by redirecting the Balloon Dog explosion away from him, after which Kiroumaru said he owed his life to Satoru; he repaid his debt by towing Group 1's canoes to the Tone River, even though he may have had orders from the Board of Education to dispose of them. After the second timeskip, Kiroumaru served as a guide for Satoru, Saki, and Inui in Tokyo to find the Psychobuster. He eventually sacrificed his life to trigger the Messiah's death feedback mechanism, on the condition that Saki and Satoru try to save the Giant Hornet queen.
- Rei: Rei is a member of Group 5 that Satoru briefly enters a romantic relationship with upon breaking up with Shun.
- Ryou Inaba: Satoru's childhood friend and a former member of Group 2, he was brought in to replace Shun after the latter's death. However, his lack of resistance to Satoru's made up stories and the lack of intimacy between them made it difficult to believe that they were ever dating.
- Tomiko Asahina: Tomiko is Satoru's grandmother, separated by nine generations. Due to the large generation gap, they do not feel like blood relatives, though Tomiko still adored him.