Holmes' application was marked "Do NOT offer admission under any circumstances," The Denver Post reported Thursday, citing documents it obtained after making a formal request through the school.
The report cited a Jan. 30, 2011, e-mail sent by Iowa Professor Daniel Tranel on the topic of seven "applicants from this past weekend," with positive comments about all but Holmes.
Tranel is director of the university's postdoctoral residency in clinical neuropsychology.
An e-mail sent by Mark Blumberg, who the newspaper said apparently served on the admissions committee with Tranel, read: "James Holmes: I agree with Dan. Don't admit."
The reason for rejecting Holmes' application was not clear, the newspaper said.
Holmes allegedly opened fire in a movie theater July 20, killing 12 patrons and injuring 58.
Holmes' attorney says he is mentally ill. Colorado prosecutors have said the former doctoral student in the University of Colorado's neuroscience program bought guns and made threats against the university after he started failing in school.
University of Colorado psychiatrist Lynn Fenton was to testify at a hearing Thursday about what court filings have characterized as "communications" between her and Holmes.