Artscroll Sefer HaChinuch (vol. 7) to this mitzvah (note 8) quotes the Minchas Yitzchak who says that the Chinuch must have had a Midrash we don't. The footnote records "some editions" who leave the man unnamed, and simply refer to him as a wise man from Amalek. "Other editions" refer to Haman's descendants who learned Torah in Bnei Brak (Gittin 57b).
The Machon Yerushalayim edition of the Minchas Chinuch also has a series of footnotes, and they, too, address this question. They quote the "some editions" from Artscroll as specifically manuscript copies of the Chinuch, with one manuscript in particular reading as does the "other editions." (They note that this manuscript has a different reading of the Gemara in Gittin than we do, and they name R' Akiva as this descendant of Haman who learned in Bnei Brak.)
The note concludes with a quote from Ein Yaakov in Sanhedrin (97b), "who reads: 'and this was R' Shmuel bar Shilas.'" It's unclear to me whether this refers to the directly preceding clause, identifying the offspring of Haman, or the earlier clauses, and R' Shmuel bar Shilas was a descendant of Amalek who might have been referred to by the Chinuch.