Following Cesena's relegation to Serie C in 1997, Hübner moved to newly promoted Serie A side Brescia, making his debut in the top Italian division in his thirties. On his debut, he scored his first goal in Serie A, against Inter at the San Siro Stadium, from an Andrea Pirlo assist, and on his second appearance, he scored a hat-trick against Sampdoria. Notwithstanding his impressive tally of 16 goals, Brescia were relegated to Serie B the following season, although he was later named the club's captain and main penalty taker, and helped the side to re-gain promotion to Serie A, scoring 21 goals during the 1999–2000 Serie B season. During the 2000–01 season, he played alongside attacking midfield playmaker Roberto Baggio, the team's new captain, under coach Carlo Mazzone, while he also faced competition as the starting striker from Igli Tare, who had a higher work-rate than Hübner. Alongside Baggio, Hübner was extremely prolific, as he scored 17 goals, helping the club to qualify for the 2001 UEFA Intertoto Cup. He was also famous for smoking on the bench during his time at Brescia, and was known for drinking grappa.