Honie was charged with aggravated murder and waived his right to a jury trial. He was sentenced to death on May 20, 1999 after a panel of judges found him guilty of first degree murder, burglary, forcible sodomy, and rape committed with a foreign object. Honie appealed his conviction on the grounds that Utah's capital punishment statute violated the 8th Amendment and the prosecution had it out for him because he was a Native American. This initial appeal failed and he tried again several years later by arguing that his attorneys did a poor job of defending him or considering the deprived circumstances of his childhood. Among these claims, Honie said he suffered from fetal alcohol syndrome and had brain damage from a head injury caused by falling from a 30 foot height as a teenager. This appeal also failed.

His execution was scheduled for August 8, 2024 and would be performed with a new experimental lethal injection cocktail of fentanyl, ketamine, and potassium chloride. Honie appealed as this was unproven and liable to cause extreme pain and that the traditional pentobarbital method should be used instead. Utah officials accepted and announced that they would execute him with pentobarbital instead. After a few final attempts to get a stay of execution, it was carried out on time after he ate a final meal consisting of a cheeseburger, fries, and a milkshake. He was the first person Utah had executed in 14 years.