Kamal Qumar Bains was charged last month following an 18-month investigation into the fatal blaze in Alder Street on February 20, 2016.
Logan Taylor, three, and Jake Casey, two, were rescued from the upstairs of the property by firefighters.
They were taken to Huddersfield Royal Infirmary, but their lives could not be saved.
Bains, 51, of Stableford Gardens, Birkby, entered not guilty pleas when he appeared at Leeds Crown Court today
A trial has been scheduled to begin on July 2 next year.