Impacts of pulsed electric fields (PEF) on physicochemical properties, bioactive compounds, and furfural and hydroxymethylfurfural (HMF) formations were quantified for sour cherry juice (SCJ). pH, titratable acidity (TA), total soluble solids (TSS), a *, b *, chroma, and total monomeric anthocyanin content (TMAC) were not significantly affected by 0–0.0341 J/L. The initial total antioxidant capacity (TAC) significantly rose with all the PEF treatments but initial citric, malic, fumaric, oxalic, succinic (−)-epicatechin, ferrulic, gallic, luteolin, p -coumaric, and o -coumaric acids, Cy-3-sop, and Cy-3-glu did not significantly degrade with no formations of furfural and HMF. The best-fit regression models explained 60.1, 39.7, and 36.3% of variation in TAC, TMAC, and TSS, respectively. Frequency exerted a greater impact than did electric field strength (EFS) on TA, pH, TSS, total color difference (TCD), hue, chroma, TMAC, TAC, sinapic, oxalic, quinic and tartaric acids, Cy-3-glu-rut, and furfural formation. 350.9 µs, 6.78 kV/cm, and 98 Hz were pointed as optimal settings.