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In this study, two strains of <i>Schizosaccharomyces pombe</i> (NCAIM Y01474^T and SBPS) and two strains of <i>Schizosaccharomyces japonicus</i> (DBVPG 6274^T, M23B) were investigated for their capacity to ferment apple juice and influence the volatile compounds of cider compared to <i>Saccharomyces cerevisiae</i> EC1118. The ethanol tolerance and deacidification capacity of <i>Schizosaccharomyces</i> yeasts could make them potential substitutes for the commonly used <i>S. cerevisiae</i> starter cultures. Despite different time courses (10–30 d), all strains could complete the fermentation process, and <i>Schizosaccharomyces</i> strains reduced the concentration of malic acid in the apple juice. Results indicated that each yeast exerted a distinctive impact on the volatile profile of the apple cider, giving final products separated using a principal component analysis. The volatile composition of the cider exhibited significant differences in the concentration of alcohols, esters, and fatty acids. Particularly, the flocculant strain <i>S. japonicus</i> M23B increased the levels of ethyl acetate (315.44 ± 73.07 mg/L), isoamyl acetate (5.99 ± 0.13 mg/L), and isoamyl alcohol (24.77 ± 15.19 mg/L), while DBVPG 6274^T incremented the levels of phenyl ethyl alcohol and methionol up to 6.19 ± 0.51 mg/L and 3.72 ± 0.71 mg/L, respectively. A large production of terpenes and ethyl esters (e.g., ethyl octanoate) was detected in the cider fermented by <i>S. cerevisiae</i> EC1118. This study demonstrates, for the first time, the possible application of <i>S. japonicus</i> in cider-making to provide products with distinctive aromatic notes”.