We report on optical and structural properties of wurtzite-phase Tm-doped GaN quantum dots (QDs) embedded in an AlN matrix, grown by plasma-assisted molecular beam epitaxy. The influence of Tm on the size and shape of the QDs is analyzed. The optical properties are studied using cathodoluminescence and photoluminescence. Intra-4f-Tm transitions from the 1D2 level show constant temperature behavior from 10 K to room temperature. The internal electric field and strains in the QDs yield a redshift and an additional broadening of the lines. We demonstrate that Tm atoms are partially located in the GaN QDs and partially at the GaN∕AlN interface.