Lawyers for Tyler Robinson argue images of him shackled and in jail clothing would spread widely in a case with extensive press coverage and public interest, which they said could prejudice future jurors.
Judge Tony Graf agreed to make some allowances to protect Robinson's presumption of innocence before a trial, agreeing the case has drawn "extraordinary" public and media attention.
"Mr Robinson shall be dressed as one who is presumed innocent," Graf said during a virtual court hearing on Monday local time.
Utah prosecutors have charged Robinson with aggravated murder in the September 10 shooting of Kirk on a college campus and plan to seek the death penalty.
While Robinson has no prior criminal history, Graf said the charges he faces are extremely serious and present safety concerns in the courtroom.
It's the court's highest priority to protect the lawyers, court staff and Robinson himself during what could be emotional hearings, Graf said before denying Robinson's request to appear without restraints.
He did, however, prohibit members of the media from photographing or filming Robinson's restraints.
Robinson is accused of firing a fatal gunshot at Kirk, a close ally of US President Donald Trump who worked to steer young voters toward conservatism, from a rooftop overlooking a crowded courtyard at Utah Valley University in Orem.
He was arrested the following night when he showed up with his parents at his hometown sheriff's office in southwest Utah, more than a three-hour drive from the site of the shooting, to turn himself in.
Prosecutors have since revealed incriminating text messages and DNA evidence they say connect Robinson to the killing.
Robinson reportedly texted his romantic partner that he targeted Kirk because he "had enough of his hatred".
Graf ordered Robinson to appear on January 16 and January 30 for his first in-person public hearings. He appeared on Monday from jail on a blacked-out screen and spoke only to confirm he was present.
8°C