In current molecular medicine, next-generation sequencing (NGS) for transcript variant detection and multivariable analyses are valid methods for evaluating gene expression, cancer mechanisms, and prognoses of patients. We conducted RNA-sequencing on samples from patients with primary central nervous system lymphoma (PCNSL) using NGS and performed multivariable analysis on gene expression data and correlations focused on Th-1/Th-2 helper T cell balance and immune checkpoint to identify diagnosis/prognosis markers and cancer immune pathways in PCNSL. We selected 84 transcript variants to limit the analysis range for Th-1/Th-2 balance and stimulatory and inhibitory checkpoints in 31 PCNSLs. Of these, 21 highly-expressed transcript variants were composed of the formulas for prognoses based on Th-1/Th-2 status and checkpoint activities. Using formulas, Th-1
low
, Th-2
high
, and stimulatory checkpoint
high
resulted in poor prognoses. Further, Th-1
high
Th-2
low
was associated with good prognoses. On the other hand, CD40-001
high
and CD70-001
high
as stimulatory genes, and LAG3-001
high
, PDCD1 (PD-1)-001/002/003
high
, and PDCD1LG2 (PD-L2)-201
low
as inhibitory genes were associated with poor prognoses. Interestingly, Th-1
high
Th-2
low
and Th-1
low
Th-2
high
were correlated with stimulatory checkpoint
low
as CD70-001
low
and inhibitory checkpoint
low
as HAVCR2 (TIM-3)-001
low
and PDCD1LG2-001/201
low
, respectively. Focused on the inhibitory checkpoint, specific variants of CD274 (PD-L1)-001 and PDCD1-002 served severe hazard ratios. In particular, PDCD1-002
high
by a cut off score was associated with poor prognoses, in addition to PDCD1-001/003
high
, PDCD1LG2-201
low
, and LAG3-001
high
. These results mainly suggest that expression of transcript variants of PDCD1 and PDCD1LG2 on the Th-1/Th-2 balance enable prognostic prediction in PCNSL. This study provides insights for development of molecular target therapies and identification of diagnosis/prognosis markers in PCNSL.