From June 2005, he continued to coach the Professional Senior Team of the FK Pelister, guiding them to a Macedonian Second League title in the 2005-06 season.
In May 2006, FK Pelister became Champions in the Macedonian Second League 2005-2006, for the first time under him, with an unbeaten record of 18 official matches in a row.
In his first season in the Macedonian First League, 2006 - 2007, FK Pelister finished in 5th position and played 1/2 final match in the National Cup.
In November 2011, Marjan Sekulovski returned to FK Pelister, bringing them to a Macedonian Second League title in the 2011-12 season and an unbeaten record of 14 official matches in a row.
[clarification needed] From January 2015 - May 2015, Ayeyawady United FC successfully played in the Myanmar National League 2015 and the AFC CUP 2015, with an unbeaten record of 15 official matches in a row.
In February 2016, Sekulovski with his new team Yangon United FC, played a second preliminary round qualification match in the Asian Champions League 2016, for the first time in history.
At the time when he left the team, Yangon United FC was in second position in MNL 2016 and already qualified in the Semifinal of the Myanmar National Cup 2016.
In December 2016, Sekulovski signed a 10-month contract for the full 2017 season with Maziya Sports and Recreation Club FC, one of the most famous and respected[by whom?]
Maziya Sport & Recreation Club FC collected 12 points in the AFC Cup competition with records of 4 wins, 0 draws, and 2 losses.
In January 2018, for the fourth time as a head coach, came back to FK Pelister from Bitola, in the Macedonian First League, to help the team survive in a difficult moment.
In September 2018, Sekulovski as Head Coach with Shan United from Myanmar became the Vice Champion (second position) of the MPT Myanmar National League 2018 with an unbeaten record of 13 official matches in a row in MPT MNL 2018 (10 win and 3 draw games), and also an unbeaten record of 15 official matches in a row in all competitions (11 win and 4 draw games), and qualified to play in AFC CUP 2019, in Group Stage.
Under Sekulovski, Maziya S&RC FC qualified for the AFC CUP 2020 Group Stage, defeating Bengaluru FC, who last season were Indian Super League 2019 champions and were AFC CUP 2016 finalists, 2:1 in Male (Maldives) on 19 February 2020 and 1:2 after full time, 2:3 after extra time, 4:3 after penalties in Bangalore (India) in a Play-Off round on 26 February 2020.
In November 2020, Marjan Sekulovski signed a long-term contract that lasted until June 2022 as head coach with Bregalnica Štip from Мacedonia.
At the moment of leaving the team, FK Pelister was in the fourth position on the table of the Macedonian Second League 2022-2023 with 30 points from 15 games.
On September 1, 2023, Sekulovski signed a contract for the upcoming 2023 / 2024 season with Sheikh Jamal DC, a team in the Bangladesh Premier League.