[6] Starting in 2013, Arthur was appointed as the assistant coach to Geoff Toovey at the Manly Warringah Sea Eagles.

As of 16 October 2013, Arthur accepted a three-year deal to join the Parramatta Eels as head coach.

In 2016, Arthur was at the forefront of the salary cap scandal which rocked the club but was praised by the media and the players for his leadership skills and managing to keep the team together.

Parramatta finished the season in 14th position but would have had enough points to qualify for the finals if not for the 12-point deduction handed to the club for breaching the salary cap.

[11][12] In the 2017 season, Arthur guided Parramatta to their first finals series since 2009 with the club finishing fourth on the premiership ladder.

[15] At the start of the 2019 NRL season, Arthur guided Parramatta to consecutive victories over Penrith and rivals Canterbury-Bankstown in the opening rounds of the competition.

In Round 6, Parramatta defeated Wests Tigers 51–6 in the opening NRL game at the new Western Sydney Stadium.

The following week on 14 May 2019, Arthur was given a two-year contract extension keeping him as head coach of the club until the end of the 2021 season.

[21] At the start of the 2020 NRL season, Arthur guided Parramatta to four consecutive victories which put the club on top of the table.

[26][27] In the 2022 NRL season, Arthur guided Parramatta to fourth place on the table which meant they qualified for the finals.

[28] On 15 March 2023, Arthur signed a two-year contract extension to remain as Parramatta head coach until the end of the 2025 NRL season.

[34] Arthur would manage to record five wins from his ten games in charge of Leeds as they finished 8th on the table and missed the playoffs.

[35] †-Parramatta were deducted 12 competition points and their for/against tally accumulated between rounds 1–9 of the 2016 season for gross long-term salary cap breaches