Using a data sample of $448\times10^{6}$ $\psi(3686)$ events collected with the BESIII detector operating at the BEPCII storage ring, the decays $\psi(3686)\rightarrow\gamma\eta$ and $\psi(3686)\rightarrow\gamma\pi^{0}$ are observed with a statistical significance of $7.3\sigma$ and $ 6.7\sigma$, respectively. The branching fractions are measured to be $\mathcal{B}(\psi(3686)\rightarrow\gamma\eta)=(0.85\pm0.18\pm0.05)\times10^{-6}$ and $\mathcal{B}(\psi(3686)\rightarrow\gamma\pi^{0})=(0.95\pm0.16\pm0.05)\times10^{-6}$. In addition, we measure the branching fraction of $\psi(3686)\rightarrow\gamma\eta'$ to be $\mathcal{B}(\psi(3686)\rightarrow\gamma\eta')=(125.1\pm2.2\pm6.2)\times 10^{-6}$ with improved precision compared to previous results.