A search for supersymmetric partners of top quarks decaying as t ˜ 1 → c χ ˜ 1 0 $$ {\tilde{t}}_1\to c{\tilde{\upchi}}_1^0 $$ and supersymmetric partners of charm quarks decaying as c ˜ 1 → c χ ˜ 1 0 $$ {\tilde{c}}_1\to c{\tilde{\upchi}}_1^0 $$ , where χ ˜ 1 0 $$ {\tilde{\upchi}}_1^0 $$ is the lightest neutralino, is presented. The search uses 36.1 fb −1 pp collision data at a centre-of-mass energy of 13 TeV collected by the ATLAS experiment at the Large Hadron Collider and is performed in final states with jets identified as containing charm hadrons. Assuming a 100% branching ratio to c χ ˜ 1 0 $$ c{\tilde{\upchi}}_1^0 $$ , top and charm squarks with masses up to 850 GeV are excluded at 95% confidence level for a massless lightest neutralino. For m t ˜ 1 , c ˜ 1 − m χ ˜ 1 0 $$ {m}_{{\tilde{t}}_1,{\tilde{c}}_1}-{m}_{{\tilde{\upchi}}_1^0} $$ < 100 GeV, top and charm squark masses up to 500 GeV are excluded.