After announcing his retirement from playing career, Toijala stayed in Kouvola with Kouvot and was named the head coach of the team in March 2006, after Risto Piipari.

The club later sued Toijala and four players under contract to the court to avoid paying them salaries for the ongoing 2018–19 season.

On 23 October 2019, Jukka Toijala was named the head coach of the Estonia senior national team.

[12] Toijala led Estonia to qualify for EuroBasket 2022 final tournament, where the team eventually finished 19th place.

[13] After a successful three-year spell, it was announced on 23 November 2022 that Toijala had extended his contract with Estonia, signing a deal until the end of February 2026.