FŠK Segesta Sisak was founded around the end of June 1906, spending most of the Interwar period in the lower divisions of the Kingdom of Yugoslavia.
With the arrival of the communist regime in 1945, the club changed its name several times, settling on SD Naprijed Sisak in 1946.
After the Republic of Croatia achieved its independence in 1991, Segesta played five consecutive seasons in the top division and even made it to the final of the 1996 UEFA Intertoto Cup.
The story goes that the club was created in late June or early July 1906 by a group of school students: 13 year old Ivo Stipčić and about twenty of his friends gathered at Ivo's uncle Ivan Šešek's inn (today's Ivana Kukuljevića-Sakcinskog Street, number 4), and decided to found a football club.
They placed first in Sisak's local league, but lost to ŠK Krajišnik Banja Luka in the quarter-finals of the provincial playoffs.
Being a provincial champion of the ZFA in those times meant Segesta was one of the better teams in Croatia and parts of Bosnia and Herzegovina.
In the return match in Solin, the hosts won 1–0, which was enough for Segesti to celebrate the club's greatest success since World War II.
Their best sports staff, coaches and players that didn't have military duties moved to their rival Segesta as the Old Lady started preparing for their first top flight campaign ever.
In the first part of the season Segesta managed an incredible 6th place, with a Prva A HNL joint best 6:0 home win against NK Rijeka, nearly missing out on the championship group but earning themselves a spot in the UEFA Intertoto Cup.
After a victorious trip to Israel against Hapoel Tel Aviv they extended their streak to 3 after wins against Stade Rennais and Luzern.
The return of Zlatko Kranjčar as manager didn't show results as Segesta ended the first half of the season in 11th.
The following season they won the Druga HNL — Središte title, but lost in the promotion playoffs to familiar foes Cibalia.
In 2001/02, they are relegated to the third division for the first time since Croatian independence, but were promoted right back after winning the 2002/03 Treća HNL — Središte title.
The formal board meeting held on the 26th of September saw Segesta's all-time best players, managers and staff receive awards.
Among the players were Slavko Draženović, Ivan Sertić, Dubravko Kahler, Željko Plepelić, Milan Radojčić, Branimir Agarević, Zoran Buinac, Nikica Valent, Josip Cavrić, Danijel Kukić and Damir Stefanovič, as well as Rudolf Draženović, the oldest living Segesta player.
Managers Stjepan Grgec and Nikola Dobranić also received awards, as well as presidents Vladimir Posavec, Dragan Boižić and Đuro Brodarac.
In November 2011, after a bad season in the third division, recent player and Segesta captain stepped into the manager role.
On the 31st of August 2016, the Croatian national football team was once again welcomed in Sisak to commemorate Segesta's 110th anniversary.
In the 2021/22 season Segesta finished 17th, and, with the expansion of the third flight into a single unified league, were once again demoted into the fourth division, where they are now playing.
Throughout the club's history, they mostly played in red and white striped kits, symbolising the colours of Pannonian Croatia.
The top part features Segesta's red and white stripes and the Croatian chequy, divided by the club name.