Harem List Part 1
Kaguya Uzumaki (SCP-001-2)
Rias Uzumaki (SCP-001-3)
Kushina Uzumaki
Dr. Amelia Buck (Main researcher of gathering information about Naruto, Rias and Kaguya)
Anna Marie (O5-1)
Tsunade Senju (O5-2)
Mei Terumi (O5-3)
Cynthia Shirona (O5-4)
Kurotsuchi Kamizuru (O5-5)
Mito Uzumaki (O5-7)
Fuuka Uzumaki (O5-8)
Tohka Yatogami (O5-9)
Saeko Busujima (O5-10)
Carol Danvers (O5-11)
Reiju Vinsmoke (O5-12)
Momoyo Kawakami (O5-13)
Kirio Hikifune (Naruto, Rias and Kaguya's personal chef)
Retsu Unohana (Naruto, Rias and Kaguya's personal doctor)
Grayfia Lucifuge (Naruto's personal head maid)
Mabui Yotsuki (Current head of the SCP Ethics Committee)
Jennifer Walters (Naruto's lawyer)
Erza Scarlet (Naruto's personal guard)
Susamaru (Naruto's personal guard, descendant of a servant of the Scarlet King and former cultist of the Children of the Scarlet King who swore loyalty to Naruto)
Rossweisse (Naruto's personal guard)
Kin Tsuchi (SCP-001/Mekhane)
Tayuya Uzumaki (SCP-001/Yaldabaoth)
Uriel the III (SCP-001/Gate Guardian)
Irene Belserion (SCP-001/Dr. Wondertaiment's good half)
Mad Moxxie (SCP-001/Dr. Wondertaiment's bad half)
Zombina (SCP-008-2)
Esdeath (SCP-009-3)
Lulu (SCP-023)
Teresa (SCP-029)
Lust (SCP-030)
Eva (SCP-040)
Abby (SCP-053)
Aqua (SCP-054)
Natasha (SCP-056)
Memeko (SCP-058)
Melona (SCP-071)
Amber (SCP-076-2)
Nemu Kurotsuchi (SCP-079)
Cassie (SCP-085)
Hachishakusama (SCP-096)
Iris Thompson (SCP-105)
Stella (SCP-134)
Alma Wade (SCP-136-2)
Rosalina (SCP-137)
Meridiana "Meri" Wojcienchowski Tellus (SCP-166)
Zinnia (SCP-169)
Karla Koitern (SCP-173)
Sauelsuesor (SCP-179)
Shion (SCP-187)
Claire Harvey (SCP-191)
Astolfo (female SCP-230)
Merlin (SCP-231-1, Sigurros' mother)
Bishanmonten (SCP-231-2; Teresa's mother)
Milim Nava (SCP-231-3; Memeko's mother)
Laura Kinney (SCP231-4; Setsuna's mother)
Wanda Maximoff (SCP-231-5; Clotho, Lachesis and Atropos' mother)
Lilly Tellus (SCP-231-6/4231-A) (she is revived and not evil)
Mitsuri Kanroji (SCP-231-7; Hope's mother)
Sigurrós Stefánsdóttir (SCP-239)
Louise Lincoln (SCP-244-2)
Yoruichi (SCP-247)
Janna Grey (SCP-273)
Rakshata Chawla (SCP-275)
Diane Bright (SCP-321 and Dr. Bright's older sister)
Lilith (SCP-336)
Felicia Hardy (SCP-347)
Baba Yaga (SCP-352)
Roberta (SCP-353)
Lucy "Wyldstyle" (SCP-387)
Guren (SCP-409-B)
Akeno Himejima (SCP-426)
Hibana (SCP-457)
Sariel (SCP-469)
Ookmai Mio (SCP-488-JP)
Dr. Margaret Sawyer-Sheen (SCP-496-J)
Illyana Rasputin (SCP-507)
Rumi Usagiyama (SCP-524)
Ororo Munroe (SCP-605)
Setsuna Tokage (SCP-682)
Chifusa Manyuu (victim of SCP-686 who can control it anomalous properties without infecting others with her milk as is it used to heal others)
Iormu (SCP-722)
Tier Harribel (SCP-734)
Sara Kujou (SCP-746)
Blair (SCP-795)
Aé Kaeru (SCP-811)
Keteru Yamiko (SCP-835-JP)
Chara (SCP-847)
Cheshire (SCP-860-2)
Ghislaine Dedoldia (SCP-939-42)
Ahri (SCP-953)
Hope (SCP-999)
Sarumaru (SCP-1000/Biggie's daughter)
Marie Talish (SCP-1337)
Noire (SCP-1471-A)
Emma Frost (SCP-1504)
Shalltear (SCP-1730 Leech Girl)
Clotho (SCP-1765-1)
Lachesis (SCP-1765-2)
Atropos (SCP-1765-3)
Jackie Barter (SCP-1903)
Phoebe (SCP-2006)
Sabrina Natsume (SCP-2241)
Beatrice (SCP-2265-5) also known as the Hanged King
Ms. Sweetie Wondertaiment (SCP-2396)
Vermeil (SCP-2521)
Elizabeth "Betsy" Braddock (SCP-2599)
Ln'eta (SCP-2662)
Camille (SCP-2747)
Faline (SCP-2845)
Mashiro (SCP-2901)
Hela (SCP-2935)
Kyure (SCP-2967)
Anantashesha (SCP-3000)
Gwenpool (SCP-3812)
Yuri (SCP-3887-A)
Rachnera (SCP-3887-B)
Rangiku Matsumoto (SCP-4205)
Kedesh-Nanaya (SCP-4960)
Arahnia Taranterra Arachnida (SCP-5683)
Medusa (SCP-6000-A)
Qukul (SCP-6004)
Boa Hancock (SCP-6360)
Kiupita (SCP-6069-A)
Miruko (SCP-6979)
Kumulipo (SCP-8000)
Estir (SCP-8001)
Nyanlathotep (SCP-8002)
Michael (SCP-8003)
Monet (SCP-8007)
Angewomon and LadyDevimon (SCP-8008)
Nemesis (SCP-017)
Machina (SCP-8099-1)
Garnet MacLaine (SCP-8099-2)
A2 (SCP-9000-A)
2B (SCP-9000-B)
Vidia (SCP-9121)
Jeunelle (SCP-9999)
Mikoto Uchiha (Naruto's godmother)
Kiyomi Uchiha (female Sasuke and Naruto's cousin)
Yor Uchiha (former Chaos Insurgency member and Kiyomi's sister)
Sarada Uchiha (Kiyomi's cousin)
Hanabi Hyuga (Naruto's cousin)
Ino Yamanaka
Samui (Naruto's cousin)
Temari Subaku (older sister of Yodo and Gaara)
Yodo Subaku (middle sister of Temari and Gaara)
Seras Victoria (former Global Occult Coalition member)
Ragyo Kiryuin (she is good in the story and is a recognized clothes designer for anomalies)
Satsuki Kiryuin
Ryuko Matoi
Medaka Kurokami
Tifa Lockhart
Aerith Gainsborough
Yuffie Kisaragi
Scarlet (Manager of the Slave Market Association as Naruto is her most frequent customer and is also an expert engineers in robotics)
Fran
Sephira
Sakura Haruno (SCP Medic with superhuman strength of Site-17)
Mebuki Haruno (Sakura Haruno's mom)
Yugito
Fuu
Tenten
Yugao Busujima Uzuki (Saeko's older sister)
Lucy Heartfilia and Rebecca Bluegarden (sisters and fans of Naruto)
Juvia Lockser
Cana Alberona
Azusa (Sigurros' familiar)
Shinobu Kocho (she can control butterflies)
Muzan Kibutsuji (female)
Kiriko (Medic)
Monika (Naruto's professional hacker)
Olivier Mira Armstrong/A'tivi
Ageha Kurono/A'ghor
Kagefusa Manyuu/A'distat
Ilulu/A'zieb
Mirajane Strauss/A'nuht
Rin/A'tellif
Orihime Inoue/A'habbat
Nejire Hado
Ochako Uraraka
Momo Yaoyorozu
Kinoko Komori
Kaina Tsutsumi
Nemuri Kayama
Yu Takeyama
Mina Ashido
Pony Tsunotori
Tsuyu Asui
Itsuka Kendo
Ruby Rose, Weiss Schnee, Blake Belladonna and Yang Xiao Long
Summer Rose, Willow Schnee, Kali Belladonna and Raven Branwen
Nico Robin
Shirahoshi
Reika Shimohira
Lara Croft
Yamato (Warrior princess)
Koyuki Kazahana (Actress)
Yuuri Kitajima (Dragonologist)
Harleen Quinzel (Psychiatrist of Site-17)
Ada Wong (Naruto's spy on the Global Occult Coalition)
Jill Valentine (Naruto's spy on the Chaos Insurgency)
Grimm
Liza Runecastle
Alipheese (Alice) Fateburn XVI
Ilias
Kirche von Anhalt Zerbst
Asuna Ichinose and Karin Kakudate (maids)
Pandora
Jay Voorhees
Freddie Krueger
Gawr Gura
Tea Gardner
Alexis Rhodes
Akiza Izinski
Anna Kaboom
Gagaga Girl
Silent Magician
Apprentice Illusion Magician
Fruit Magician Girls (Apple, Choco, Citri and Kiwi)
Sailor Guardians (Rei Hino, Usagi Tsukino, Minako Aino, Ami Mizuno and Makoto Kino)
Azula
Ty Lee
June
Katsuragi, Ikaruga, Asuka, Hibari and Yagyu
Sayuri (younger)
Homura
Haruka
Yumi
Noelle Silva
Maki Oze
Tamaki Kotatsu
Glynda Goodwitch
Salem
Neopolitan
Carmine Esclados
Venelana Gremory
Xenovia Quarta
Kuroka
Irina Shidou
Asia Argento
Yasaka
Kunou (older)
Ophis
Moka Akashiya (half-demon)
Kurumu Kurono
Mizore Shirayuki
Tsurara Shirayuki
Makoto Nanaya
Konoe Ayatsuki Mercury
Baiken
Cammy White
Chun-Li
With more on the way.