Abstract Emission-line galaxies (ELGs) are crucial for understanding the formation and evolution of galaxies, while little is known about their variability. Here we report on the optical variability of a sample of ELGs selected in the COSMOS field, which has narrowband observations in two epochs separated by ≳12 yr. This sample was observed with the Suprime-Cam (SC) and Hyper Suprime-Cam (HSC) on the Subaru telescope in NB816 and i ′ / i bands, respectively. After carefully removing the wing effect of a narrowband filter, we check the optical variability in a sample of 181 spectroscopically confirmed ELGs. We find that 0 (0/68) Hα emitters, 11.9% (5/42) [O iii] emitters, and 0 (0/71) [O ii] emitters show significant variability ( ∣ Δ m NB ∣ ≥ 3 σ Δ m NB , AGN = 0.20 mag ) in the two-epoch narrowband observations. We investigate the presence of active galactic nuclei (AGN) in this variable ELG (var-ELG) sample with three methods, including X-ray luminosity, mid-infrared activity, and radio excess. We find zero bright AGN in this var-ELG sample but cannot rule out the contribution from faint AGN. We find that supernovae explosions (SNe) could also dominate the variability of the var-ELG sample. The merger morphology shown in the HST/F814W images of the entire var-ELG sample is in agreement with the enhancement of star formation, i.e., the SNe activity.