As a coach, Jacobsen won the 2013 Danish Handball League with Aalborg Håndbold, and led Rhein-Neckar Löwen to back-to-back German Handball-Bundesliga championships in the 2016 and 2017 season.

Born in Viborg, Nikolaj Jacobsen moved with his parents to Southern Funen as a child, and began playing handball at the age of 11.

[5] Having played youth handball at GOG Håndbold, Nikolaj Jacobsen made his senior debut for the club in 1990, at the age of 18.

Jacobsen scored 189 goals in 28 Bundesliga matches during the 1998 season,[9] though Bayer Dormagen finished in 14th placed, and were eventually relegated.

[6] The temperamental Jacobsen was also taught to be a team player, by his new Swedish teammates Magnus Wislander, Staffan Olsson and Stefan Lövgren.

[11] In the following three seasons, Jacobsen scored 1015 goals in a total 142 games for Kiel,[9] as the club won two Handball Bundesliga championships and two German Cup titles.

Kiel also finished second in the international 1999–2000 EHF Champions League tournament, losing 52–54 on aggregate to FC Barcelona Handbol in the final.

[9] In the opening game of the 2001–02 Bundesliga season, Jacobsen injured his knee when he collided with the goalkeeper of opposing team SG Wallau/Massenheim.

The injury also meant, that Jacobsen was absent from the Denmark team which won bronze medals at the 2002 European Championship.

[15] Jacobsen scored 71 goals in 28 league games for Viborg during his time at the club,[9] but focused increasingly on his role as assistant coach.

[16] It was time for Jacobsen to become head coach,[15] and he moved to Danish Handball League team Aalborg Håndbold in 2012.