The two-volume set LNCS 12043 and 12044 constitutes revised selected papers from the 13th International Conference on Parallel Processing and Applied Mathematics, PPAM 2019, held in Bialystok, Poland, in September 2019. The 91 regular papers presented in these volumes were selected from 161 submissions. For regular tracks of the conference, 41 papers were selected from 89 submissions. The papers were organized in topical sections named as follows: Part I: numerical algorithms and parallel scientific computing; emerging HPC architectures; performance analysis and scheduling in HPC systems; environments and frameworks for parallel/distributed/cloud computing; applications of parallel computing; parallel non-numerical algorithms; soft computing with applications; special session on GPU computing; special session on parallel matrix factorizations. Part II: workshop on language-based parallel programming models (WLPP 2019); workshop on models algorithms and methodologies for hybrid parallelism in new HPC systems; workshop on power and energy aspects of computations (PEAC 2019); special session on tools for energy efficient computing; workshop on scheduling for parallel computing (SPC 2019); workshop on applied high performance numerical algorithms for PDEs; minisymposium on HPC applications in physical sciences; minisymposium on high performance computing interval methods; workshop on complex collective systems. Chapters "Parallel Adaptive Cross Approximation for the Multi-trace Formulation of Scattering Problems" and "A High-Order Discontinuous Galerkin Solver with Dynamic Adaptive Mesh Refinement to Simulate Cloud Formation Processes" are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.