9-Hydroxymethylxanthene derivatives were optimized as a photolabile protecting group for amines in flow chemistry. 9-Methylxanthene and 2-methoxy-9-methylxanthene showed excellent deprotection yields in protic and aprotic solvents, respectively. The protecting group has good stability in acidic, basic, and thermal conditions and was successfully utilized for protection and deprotection of a variety of amines. A multistep continuous-flow synthesis of a piperazinylcarbonyl-piperidine derivative utilized the 2-methoxy-9-methylxanthene as the key protecting group utilized in an orthogonal manner.