Using 6.32~fb$^{-1}$ of $e^+e^-$ collision data recorded by the BESIII detector at center-of-mass energies between $4.178$ to $4.226$~GeV, we present the first measurement of the decay $D_s^+\to f_0(980)e^+\nu_e,\,f_0(980)\to \pi^0\pi^0$. The product branching fraction of $D_s^+\to f_0(980)e^+\nu_e,\,f_0(980)\to \pi^0\pi^0$ is measured to be $(7.9\pm1.4_{\rm stat} \pm0.3_{\rm syst})\times 10^{-4}$, with a statistical significance of $7.8\sigma$. Furthermore, the upper limits on the product branching fractions of $D_s^+\to f_0(500)e^+\nu_e$ with $f_0(500)\to \pi^0\pi^0$ and the branching fraction of $D_s^+\to K_{S}^{0}K_{S}^{0}e^+\nu_e$ are set to be $6.4\times 10^{-4}$ and $3.9\times 10^{-4}$ at 90\% confidence level, respectively. Our results provide valuable inputs to the understanding of the structures of light scalar mesons.