For the second league match in a row, the 22-year-old Slovenian was the match-winner for the English club, which continues to rise under the leadership of Michael Carrick.
Sesko scored the game's only goal at Everton in the 71st minute, lifting United to fourth place in the table. Everton are ninth after 27 of 38 matches.
Manchester United have yet to lose under interim manager Michael Carrick, who took over after the club sacked Ruben Amorim in January.
Benjamin Sesko also scored in a 1–1 draw at West Ham a couple of weeks ago.
