NTRKfusions are validated oncogenic drivers of various adult and pediatric tumor types, including thyroid cancer, and serve as a therapeutic target. Recently, tropomyosin receptor kinase (TRK) inhibitors, such as entrectinib and larotrectinib, display promising therapeutic efficacy inNTRK-positive solid tumors. Although someNTRKfusion partners have been identified in thyroid cancer, the spectrum ofNTRKfusion is not fully characterized. In this study, a dualNTRK3fusion was identified by targeted RNA-Seq in a 47-year-old female patient with papillary thyroid carcinoma. The patient harbors a novel in-frame fusion betweenNTRK3exon 13 andAJUBAexon 2, co-existing with a known in-frame fusion betweenETV6exon 4 andNTRK3exon 14. The dualNTRK3fusion was validated by Sanger sequencing and fluorescencein situhybridization (FISH) but lack TRK protein expression as defined by pan-TRK immunohistochemistry (IHC). We supposed the pan-TRK IHC result to be falsely negative. In conclusion, we present the first case of a novelNTRK3-AJUBAfusion co-existing with a knownETV6-NTRK3fusion in thyroid cancer. These findings extend the spectrum of translocation partners inNTRK3fusion, and the effect of dualNTRK3fusion on TRK inhibitor therapy and prognosis needs long-term follow-up.