Philadelphia chromosome positive B cell lymphoblastic lymphoma (Ph+ B-LBL) is an extremely rare disease. We report a 27-year-old patient diagnosed with primary testicular and cutaneous Ph+ B-LBL without bone marrow involvement. The CCCG-LBL-2016 regimen (https://clinicaltrials.gov/ct2/show/NCT02845882) was initially administered due to the fast pathological diagnosis as B-LBL that was first obtained. To identify potential therapeutic targets, RNA sequencing (RNAseq) was also performed on lymph node specimens as a part of the routine diagnostic workup in our center. Unexpectedly, IKZF1 deletions and BCR-ABL1 fusion transcripts were detected. Based on these results, we retrospectively performed fluorescence in situ hybridization (FISH) for BCR/ABL1 rearrangements in the same lymph node specimen, and a 70% positive signal was detected. The patient subsequently received the CCCG-LBL-2016 protocol combined with the BCR-ABL tyrosine kinase inhibitor (TKI) dasatinib, along with prophylactic intrathecal infusion. Then, the patient underwent TBI-based haploidentical (haplo) allogeneic hematopoietic stem cell transplantation (haplo-allo-HSCT) as consolidation following the achievement of remission and continued taking dasatinib as maintenance therapy. The patient was still in complete remission 1 year after diagnosis. This case indicates that the detection of potential molecular targets, especially those targets that can be pharmacologically treated, such as BCR/ABL1 fusion transcripts, is of important value to both LBL diagnosis and therapeutic strategy choices. FISH, reverse transcriptase polymerase chain reaction (RT-PCR) and/or RNAseq should be routinely carried out in lymphoma specimens to depict its genetic landscape for the further execution of a precise therapy strategy.