For the first time since his international-competition debut at 2013's WC, Shirai did not qualify for the Japanese men's national AG team; thus, the inability to compete at the 2019 Artistic Gymnastics World Championships in Stuttgart, Germany, on October 4–13, 2019. Shirai's performances were slowed for most of the 2019 season by a rather stubborn and nagging left ankle injury, resulting in him not being able to compete the very best during 2019's All-Japan Apparatus Championships that the results there and at the 2019 NHK Trophy determined a gymnast's eligibility to join the Japanese national team at 2019's WC. Shirai's best chance was getting one of two spots available on specialist apparatus individuals, specifically the signature events on FX and VT. However, Shirai just managed 3rd place on FX, and 5th on VT that made him not qualify for the WC, and was not able to defend his world medals from 2018. Also, as Shirai was not the only high-profile absentee (Kōhei Uchimura not there either due to injuries), the Japanese men had sent a fairly inexperienced squad to the 2019 WC where men's competition was dominated by other countries. Shirai worked hard on returning to competition form for an extended time period of attempting to recover from various injuries, and then got quite rusty on every event.