It is quite often claimed that Japanese has only two irregular verbs. However, there are more than ten verbs in modern Japanese which conjugate irregularly.
Both suru (to do) and kuru (to come) are highly irregular verbs. None of their conjugations follow the standard patterns.
See a textbook or reference book for full details.
In Japanese grammar, suru is called a sahen (サ変) verb, and kuru is called a kahen (カ変) verb. There are no other sahen or kahen verbs.
Iku (to go) has irregular te form and past tense itte, and itta; if iku was regular, the te form and past tense would be iite and iita respectively.
The honorific verbs irassharu, ossharu, kudasaru, gozaru, nasaru (see What is Japanese respect language?) all have an irregular stem, where the ru ending conjugates as i rather than ri. For example, the gozaimasu of arigatō gozaimasu, "thank you". If this conjugated as a regular verb it would conjugate as gozarimasu.
Kureru has an irregular imperative form kure. If it was regular, the imperative would be kureyo or kurero.
Aru, "to have", "to be", is mostly regular, but for its negative nai is used, rather than aranai.
Iu is irregular in its pronunciation, varying between yuu and iu.
Some suru verbs (see What is a suru verb?), verbs made by adding suru to a noun, conjugate as if they were two verbs. For example, aisuru "to love" (see How can I say "I love you" in Japanese?) may conjugate as aisuru and aisu, depending on the form. aisu is used for the potential form aiseru "can love", instead of aidekiru. Similarly for verbs such as yakusu (translate).
Tou (問う) has an irregular te-form toute (問うて) and past tense touta (問うた).
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