Bouchalakis started his football career attending the Ergotelis Football Academy, the youth system of his local Superleague club Ergotelis. His performances with the club's youth teams in the Greek Superleague Youth Leagues led the club's board of directors to promote him to the first team on 19 May 2011, when he signed his first professional contract with the club at the age of 18. He eventually made his debut on 11 December 2011, in a game against Doxa Drama. During the summer of 2012, Bouchalakis earned the trust of manager Siniša Gogić and became a regular starter for the club during their short tenure in the Greek Football League. His good performances reportedly drew the attention of many clubs, both in Greece and abroad. Eventually, Greek giants Olympiacos acquired his rights from Ergotelis on 22 March 2013 for a reported €150K, following up on the acquisition of Bouchalakis' fellow Ergotelis teammate Manolis Tzanakakis. As part of the deal, both players were allowed to finish the season with Ergotelis, who also acquired the right re-sign both players on loan in the following season. Bouchalakis was instrumental in helping the club return to the Superleague at the end of the 2012–13 season, summing up 40 caps in both the Football League and Greek Cup competitions and managing to score 6 goals while dishing out two assists. After Bouchalakis' and Tzanakakis' transfers were announced by Olympiacos, the club's board of directors decided to green-light the loan deal with Ergotelis, who added both players to their roster for the 2013–14 Superleague season in order for them to receive substantial playing time in top-flight in a familiar environment. Bouchalakis contributed to Ergotelis' all-time best 7th place finish with 30 caps and 2 goals. He returned to Olympiacos in the summer of 2014 to earn a spot in the champions' roster for next season.
Olympiacos
Bouchalakis scored from long distance in a 3–0 win against Milan in the 2014 International Champions Cup. On the beginning of the 2015–16 season, Bouchalakis tried his best to convince his coach Marco Silva to stay in the club. His contract was extended in 2016 until the summer of 2020.
After a trial in pre-season, Bouchalakis signed a three-year deal with EFL Championship club Nottingham Forest in July 2017. As Forest and Olympiacos had the same owner, there was no transfer fee. He scored twice on his league debut as Forest won 4–3 away to Brentford on 12 August. He played regularly in the first half of the season but lost his place under new manager Aitor Karanka.
