This work aimed to assess novel protective roles and regulation of Spy1, a histidine-containing phosphotransfer (HPt) protein, in the fission yeast Schizosaccharomyces pombe. The structural gene encoding Spy1 was cloned into the shuttle vector pRS316 to generate the recombinant plasmid pYFSpy1. The spy1(+) mRNA level was notably increased in S. pombe cells harboring the plasmid pYFSpy1. The S. pombe cells harboring pYFSpy1 exhibited higher survival than the vector control cells on the minimal media plates with nitric oxide (NO)-generating sodium nitroprusside (SNP) or without nitrogen source. In the liquid minimal media, they also showed higher viability under nitrosative stress or nitrogen-starved condition. The intracellular reactive oxygen species (ROS) level appeared to be lower in the fission yeast cells harboring pYFSpy1 than in the control yeast cells. Overexpression of the spy1(+) gene showed scavenging effect on NO generated from SNP. Synthesis of β-galactosidase from the spy1(+)-lacZ fusion gene was significantly enhanced by SNP and nitrogen starvation in the Pap1-positive but not in the Pap1-negative cells. The spy1(+) mRNA level in S. pombe was also elevated by SNP and nitrogen starvation in the Pap1-positive but not in the Pap1-negative cells. In summary, Spy1 plays protective roles against nitrosative and nutritional stress in the fission yeast and is transcriptionally up-regulated by nitrosative and nutritional stresses in a Pap1-dependent manner.