Phakopsora pachyrhizi, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of P. pachyrhizi candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial de novo assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts at 3, 7, 10, and 14 days after inoculation, respectively. We identified a repertoire of CSEPs of which a majority was expressed during the later stages of infection, and many that could be bioinformatically associated with haustoria. This approach for identifying CSEPs improves our current understanding of the P. pachyrhizi effectorome, and these CSEPs are expected to be a valuable resource for future studies of P. pachyrhizi-soybean interactions.