In her sophomore year, she was a starter in every game, and upped her scoring average to 22 points per game. In that year, her team's record was 18–4. As a junior, she helped lead her team to the state AA public school title, with a 22–3 record for the year. Stewart averaged 24 points and 15 rebounds for the season. During her junior year, she announced that she would be attending the University of Connecticut. The day after the announcement, she dunked the ball in a game against Baldwinsville, her first career dunk. Stewart achieved a milestone on January 31, 2012, when she scored her 2,000th point, as part of a 31–0 run against Auburn.
Stewart was selected as a member of the 2012 McDonald's All-American team, which represented the 24 best female high school basketball players. The selected players were grouped into two squads that competed in the annual McDonald's All-American Game, held that year in Chicago. Stewart was selected to the 2012 Women's Basketball Coaches Association (WBCA) High School Coaches' All-America Team. The top 20 high school players in the country were named as WBCA All-Americans and were eligible to play in the all-star game. She participated in the 2012 WBCA High School All-America Game, scoring 10 points. Stewart was named the 2012 Naismith High School Girls' Player of the Year, the honor awarded by the Atlanta Tipoff Club to the best female high school basketball player in the country. In March 2012, in a surprise presentation by Tamika Catchings, Stewart received the Gatorade National Girls Basketball Player of the Year award. Stewart was one of six finalists for the Gatorade High School Athlete of the Year.
Stewart was named to the USA Basketball U-18 team. She joined future UConn teammates Moriah Jefferson and Morgan Tuck on the 12-player squad that competed in the 2012 FIBA Americas U-18 National Championship, held in August 2012, in Puerto Rico. Stewart was the youngest, and only high school player, on the 2011 USA Women's Pan American Games team, but was the player with the most international experience on the team. The team started by winning their first four games with margins of victory of 40 points or more. This set up the championship game against Brazil. The team from Brazil started strong, and held a double-digit lead early in the game. After scoring only seven points in the first quarter, the team scored 21 or more in the next three quarters and reclaimed the lead. The USA won 71–47 to claim the gold medal.