Liam Whoriskey, a 25-year-old from Glenabbey Gardens in the city, was also found guilty of one charge of child cruelty.
The three-year-old was found dead in his bed in his family flat at Colmcille Court in the Bogside on Sunday, September 17, 2017, around 10 am.
The jury of six men and five women returned unanimous verdicts after 80 minutes of deliberation.
Family and friends of the toddler roared and clapped in a packed public gallery when the verdicts were announced.
The judge excused the 11 jurors for life and said he would sentence Whoriskey following a plea hearing on Thursday, November 29.
It had been the prosecution case that Kayden died as a result of 15 blunt force trauma injuries to his head and were “non-accidental”.
But a medical expert called by the defence said it could not be stated exactly when the child’s injuries had been sustained.