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Rei Ayanami and Shinji Ikari are supposed to be brother and sister. Why do they not both have the same surname as their father, Gendo Ikari?

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They are not supposed to be brother and sister. Rei was created using material of Yui Ikari which would make their relationship closer to mother/son or aunt/nephew genetically speaking and this origin was kept secret.

Gendō Ikari brought his first clone (Rei I) to the Gehirn base, which is the predecessor of NERV and responsible for the development and construction of the first Evangelion units, introducing her as the daughter that an acquaintance entrusted to him.
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Officially, Rei II is chosen by an organization called the Marduk Institute as the First Child and pilot of EVA Unit-00, though this organization is later revealed to be a front, with Gendō and the SEELE council pulling all the strings.

So officially there is no relation between Gendo and Rei except that he is responsible for her. Giving her his surname would serve no purpose and instead make others more suspicious of her and what connection she shares with him.

Quote from Wikipedia

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  • Shinji and Rei are biologically half-siblings since they share their mother (with a different biological father), and while Gendo has no biological relationship with Rei, she's his step-daughter since she's his wife's daughter.
    – nick012000
    Sep 6 '20 at 16:14
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    You can choose to look at it that way, but that's not actually how step- relationships work. If, for example, Alice gets a divorce from Bob, and then marries Chet, and then Alice and Chet have a son, Daniel -- Bob is not Daniel's step-father. Now, Rei doesn't have a biological father or mother; as stated, she's a being created from the genetic material of Yui and Lilith. Half-siblings is oversimplifying the relationship between Rei and Shinji; she could also be considered his mother (as a clone of her) or his aunt (as a clone "sibling" of her, like her twin). Sep 21 '20 at 20:31
  • Further, Gendo is (probably?) Rei's legal guardian, so on paper she and Shinji may be step-siblings. It's a very tangled family tree, is what I'm saying. Sep 21 '20 at 20:37

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