SG Flensburg-Handewitt acquired their first major trophy with the 1996/1997 EHF Cup by defeating Danish side Virum-Sorgenfri HK 52–42 on aggregate in the final.

Three consecutive DHB-Pokal titles (2003/04 vs TUSEM Essen, 2004/05 vs HSV Hamburg, and 2005/06 vs THW Kiel) followed, as did success in the league, with a championship victory in the 2003/04 season.

Slovenian club RK Celje did however, prevent a third trophy that year for SG by winning the 2003-04 EHF Champions League final against them.

In 2010, former player Ljubomir Vranjes became the new coach and it was under him that SG Flensburg-Handewitt won the EHF Champions League final at their third attempt, beating THW Kiel 30–28 at the Lanxess Arena in Cologne.

They were defeated 38–31 by Rhein-Neckar Löwen in the DHB-Pokal semi-finals, 35–27 at Flens-Arena by BM Granollers in the EHF European League quarter-finals, and then 29–19 by THW Kiel in the Nordderby in a crucial Handball-Bundesliga game.

In the 2023-24 season with Nicolej Krickau as head coach, Flensburg missed out on qualification for the 2024-25 EHF Champions League by finishing 3rd in the Handball-Bundesliga.

SG Flensburg-Handewitt holds a reputation as being a perennial "second-place" club – with three league titles the team has also finished runner-up fourteen times.

Due to their proximity to Scandinavia, SG typically have top international players from Denmark, Sweden and Norway in their squad.

SG Flensburg-Handewitt have sporting partnerships with SønderjyskE Herrehåndbold, VfL Lübeck-Schwartau, Lugi Handboll, DHK Flensborg and Flensburg Academy.

Note: All five matches which could not be played due to COVID-19 restrictions were adjudicated by the EHF as 10–0 losses for the club which could not field a full team.