The Tigers preserved their place in the Championship on the final day of the season on goal difference, having been bottom when Selles took over in December.
The 41-year-old Spaniard is the third manager sacked by Hull owner Acun Ilicali in the last 12 months, with the northern club now starting their search for a fifth permanent boss since the Turkish media tycoon took control in early 2022.
"Following a thorough review of football operations after a challenging campaign, the club feels a change in leadership is necessary to move the team forward in line with our ambitions," said a Hull statement.
Hull went into the final day of the season in the bottom three but a 1-1 draw at Portsmouth kept them in the Championship, the division below the elite Premier League, with Selles winning nine of his 27 league games in charge.