Phillip Simmons, 38, of May Street, has been charged with two counts of murder and one of burglary.
The bodies of Daniel Hatfield, 52 and Matthew Higgins, 49 were found at a house on May Street with "significant multiple injuries" on Friday.
Mr Simmons is due at Hull Crown Court on Wednesday.
He was remanded in custody when he appeared before Hull magistrates earlier.
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Two women also arrested in connection with the deaths have been released from custody.
A 36-year-old woman has been released on police bail until next month and a 27-year-old woman has been released unconditionally.
A man has been charged with a double murder following the discovery of two bodies in the garden of a house in Hull.