Having retired from football, Pahars entered a career in coaching, starting as assistant at Skonto, which resulted in his first appointment as a manager.

He had a trial in a reserve team match against Oxford United on 10 February 1999 in which he scored a perfect hat-trick – a header and a goal with each foot in a 7–1 victory.

Southampton agreed a fee with Skonto of around £800,000 and, despite difficulties in obtaining a work permit and objections from the PFA, these problems were overcome and he joined the Saints in March 1999, thus becoming the first Latvian to play in the Premier League.

By now, Dave Jones had been replaced as manager by Glenn Hoddle, who decided to move Pahars to a wide position, with the theory that he could scare the opposition, with his dribbling and pace, and provide for others as well as score himself.

After an impressive start to the 2000–01 season – finding the net six times as a striker, he returned to a deeper role, and his form slumped as a result.

He was still a threat providing his teammates with opportunities, but his form was patchy and inconsistent and he only found the net three more times to take his tally for the season to nine goals.

He scored at a regular rate over the next three months including the winner in a 1–0 victory over Charlton Athletic on 24 November – the Saints first win in their new St Mary's Stadium.

In the summer of 2002, Pahars required a hernia operation, which forced him to miss the whole of pre-season and although he scored a penalty in a 1–0 home win over Everton on 11 September, he never fully recovered from his injury.

With that as an added incentive to get himself fully fit, he found himself back in the Saints starting line up for three successive games, which all ended in victories.

Comebacks for the reserves were promising, until problems flared up again, causing him to miss the whole of the season in frustrating circumstances, as the Saints were relegated after 28 years in the top flight of English Football.

In July 2006 Pahars signed with Anorthosis Famagusta, a Cypriot team managed by former Georgian International Temuri Ketsbaia.

During a spell of injuries, he managed to play in the closing minutes as Latvia claimed a place in the European Championships in 2004 with a 2–2 draw in Turkey on 19 November 2003.

With so many injury problems over the season, he was a substitute for all three of 2004 UEFA Latvia's Group matches at Euro 2004, although he did taste the championships by coming off the bench in all three games.

Not long after his appointment, on 11 July 2013, Pahars was promoted, becoming the manager of the nation's senior team, shortly after Aleksandrs Starkovs vacated his position.