Mack Beggs, an 18-year-old senior from Euless Trinity High School near Dallas, entered the tournament in Cypress outside of Houston with an undefeated record.
He overcame Chelsea Sanchez, who he also beat for the title in 2017, in the final of the 110lbs division on Saturday, but video of the competition shows many spectators reacted angrily to his victory.
Mr Beggs is in the process of transitioning from female to male and is taking a low-dose of testosterone.
The wrestler has repeatedly asked authorities to compete in the boys’ division, but rules for Texas public high schools require athletes to enter tournaments under the gender on their birth certificate.
"He has so much respect for all the girls he wrestles," said his mother, Angela McNew. “People think Mack has been beating up on girls. The girls he wrestles with, they are tough.
“It has more to do with skill and discipline than strength."
Steroid therapy treatments Mr Beggs was receiving while wrestling girls sparked a fierce debate about competitive fairness and transgender rights ahead of the competition last year.
His road to the championship included two forfeits by wrestlers, who pulled out over fears of sustaining a head injury.
Only one wrestler refused to compete against Mr Beggs during his march to the state title this year, but he was subject to a lawsuit by a group of parents attempting to block his participation.
Rules restricting athletes to competing as the gender on their birth certificate were approved in 2016 by the University Interscholastic League, the governing body for Texas high school sports.
It was done to help schools determine competition, Jamie Harrison, the UIL's deputy director said.
The latest win means Mr Beggs completes his high school wrestling career with an undefeated record, racking up 35 wins over his last season.
He will now move on to college, where NCCA regulations will allow him to enter competitions in the men’s division.
Additional reporting by Associated Press