There is an official guide available that describes how to handle RNA-seq data with GSEA.
Normalizing RNA-seq quantification to support comparisons of a
feature's expression levels across samples is important for GSEA.
Normalization methods (such as, TMM, geometric mean) which operate on
raw counts data should be applied prior to running GSEA. Tools such as
DESeq2 can be made to produce properly normalized data (normalized
counts) which are compatible with GSEA.
For RNA-Seq data, you will need normalize and filter out low count measurements, and perform other preprocessing as needed.