Context. Stellar activity mitigation is one of the major challenges for the detection of earth-like exoplanets in radial velocity measurements. Several promising techniques are now investigating the use of spectral time-series, to differentiate between stellar and planetary perturbations. In this context, developing a software that can efficiently explore the parameter space of stellar activity at the spectral level is of great importance. Aims. The goal of this paper is to present a new version of the Spot Oscillation And Planet (SOAP) 2.0 code that can model stellar activity at the spectral level using graphical processing units (GPUs). Methods. We take advantage of the computational power of GPUs to optimise the computationally expensive algorithms behind the original SOAP 2.0 code. For that purpose, we developed GPU kernels that allow to model stellar activity on any given wavelength range. In addition to the treatment of stellar activity at the spectral level, SOAP-GPU also includes the change of spectral line bisectors from center to limb, and can take as input PHOENIX spectra to model the quiet photosphere, spots and faculae, which allow to simulate stellar activity for a wider space in stellar properties. Results. Benchmark calculations show that for the same accuracy, this new code improves the computational speed by a factor of 60 compared with a modified version of SOAP 2.0 that generates spectra, when modeling stellar activity on the full visible spectral range with a resolution of R=115'000. Although the code now includes the variation of spectral line bisector with center-to-limb angle, the effect on the derived RVs is small. We also show that it is not possible to fully separate the flux from the convective blueshift effect when modeling spots, due to their lower temperature and thus the appearance of molecular absorption in their spectra. Rather negligible for the Sun, this degeneracy between the flux and convective blueshift effect become more important when we move to cooler stars, however, this issue does not impact the estimation of the total effect (flux plus convection), and therefore users can trust this output. Conclusions. The publicly available SOAP-GPU code allows to efficiently model stellar activity at the spectral level, which is essential to test further stellar activity mitigation techniques working at the level of spectral timeseries not affected by other sources of noise. Besides a huge gain in performance, SOAP-GPU also includes more physics and is able to model different stars than the Sun, from F to K dwarfs, thanks to the use of the PHOENIX spectral library. We however note that due to the limited understanding of stellar convection and activity on other stars than the Sun, the more we go away from the solar case, the more the output of the code should be taken with care.