Rudan was again a key figure in the 1999–00 season, playing 22 games, a less successful year for the club, slumping to the bottom half of the table.

In mid-2000, unhappy with his situation at Spirit, Rudan bought out the remainder of his contract and moved to German second division club Alemannia Aachen on a free transfer.

It was revealed that persons claiming to represent Rudan and Northern Spirit collected DM 290,000 in a suitcase from Aachen as a transfer fee.

Now a seasoned player with international experience, Rudan appeared regularly for the NSL club throughout the 2002–03 calendar but could not help them reach the finals round.

Rudan captained the side through the group matches, playing all six games, and drawing upon his previous experiences in Asian football.

In December 2007, Rudan signed a deal with J2 League side Avispa Fukuoka, linking up with his former coach of Sydney FC Pierre Littbarski and replacing former teammate Alvin Ceccoli.

[12] On 6 January 2009, Rudan signed for Axpo Super League (Switzerland 1st division) team FC Vaduz, based in Liechtenstein on a free transfer.

He left Adelaide after their final group game in the AFC Champions League as he announced his retirement as a player, and intends to move into coaching.

[14] Rudan's footballing talent was first recognised in 1992 as he was granted a place in the AIS program, aimed at developing players for national youth teams.

Rudan was made vice captain to Mark Viduka in Australia's undefeated Youth World Cup qualifying campaign and scored the only goal of the Oceania final against New Zealand.

As part of the squad for the 1995 Youth World Cup, Rudan played three of Australia's four matches including their second round exit in extra time at the hands of Portugal.

On 30 May 2018, it was announced that Rudan has signed a two-year deal as head coach of Wellington Phoenix who play in the Australian A-League.

[20] After disappointing results from Rounds 3 to 5, Wellington Phoenix drew 1–1 with league leaders Perth Glory in which he criticised the referee and the VAR for biased decisions, but no actions were taken.

Western United won their inaugural A-League finals match, defeating Brisbane Roar 1–0, before losing by the same scoreline to Melbourne City in the semi-final days later.

[25] On 31 January 2022, Rudan was announced as the interim head coach of the Western Sydney Wanderers A-League men's team until the end of the 2021–22 season.

[26] The Wanderers made a bright start to life under new management, beating Perth Glory 1–0 in Mark Rudan’s first game in charge.