The brown alga Saccharina japonica is widely consumed in Asian countries, and post-harvest drying methods such as sun drying and oven drying are commonly used to extend the shelf life of S. japonica. Thus, the present study analyzed the ethanol extract and organic solvent fractions of S. japonica to examine the effects of UVA and heating on certain bioactive compounds (fucoxanthin, phlorotannin compounds, and total antioxidants) during the drying process. The fucoxanthin contents in the ethanol extract and different solvent fractions significantly decreased in response to UVA. However, fucoxanthin in the ethanol extract and other fractions showed resistance to thermal treatment. It is noteworthy that the total phlorotannin content (TPC) in the ethanol extract and all fractions showed an approximately 2.5-fold increase upon UVA radiation. The TPC also increased in all samples exposed to high temperatures, except for those in the chloroform fraction. The total antioxidant capacity (TAC) also exhibited significant increases in a pattern similar to the TPC. The findings demonstrate that UVA exposure and heating stimulated the degradation of fucoxanthin while it increased the TPC and TAC in the extract and fractions of S. japonica.