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We report on small-amplitude optical variability and recent dissipation of the unusually persistent broad emission lines in the blue compact dwarf galaxy PHL 293B. The galaxy's unusual spectral features (P Cygni-like profiles with $\sim$800 km s$^{-1}$ blueshifted absorption lines) have resulted in conflicting interpretations of the nature of this source in the literature. However, analysis of new Gemini spectroscopy reveals the broad emission has begun to fade after being persistent for over a decade prior. Precise difference imaging light curves constructed with the Sloan Digital Sky Survey and the Dark Energy Survey reveal small-amplitude optical variability of $\sim$0.1 mag in the g band offset by $100\pm21$ pc from the brightest pixel of the host. The light curve is well-described by an active galactic nuclei (AGN)-like damped random walk process. However, we conclude that the origin of the optical variability and spectral features of PHL 293B is due to a long-lived stellar transient, likely a Type IIn supernova or non-terminal outburst, mimicking long-term AGN-like variability. This work highlights the challenges of discriminating between scenarios in such extreme environments, relevant to searches for AGNs in dwarf galaxies. This is the second long-lived transient discovered in a blue compact dwarf, after SDSS1133. Our result implies such long-lived stellar transients may be more common in metal-deficient galaxies. Systematic searches for low-level variability in dwarf galaxies will be possible with the upcoming Legacy Survey of Space and Time at Vera C. Rubin Observatory.