In Biswas et al (2006 J. Cosmol. Astropart. Phys. JCAP03(2006)009 [hep-th/0508194]) it was shown how non-perturbative corrections to gravity can resolve the big bang singularity, leading to a bouncing universe. Depending on the scale of the non-perturbative corrections, the temperature at the bounce may be close to or higher than the Hagedorn temperature. If matter is made up of strings, then massive string states will be excited near the bounce, and the bounce will occur inside (or at the onset of) the Hagedorn phase for string matter. As we discuss in this paper, in this case cosmological fluctuations can be generated via the string gas mechanism recently proposed in Nayeri et al (2005 Preprint hep-th/0511140). In fact, the model discussed here demonstrates explicitly that it is possible to realize the assumptions made in Nayeri et al (2005 Preprint hep-th/0511140) in the context of a concrete set of dynamical background equations. We also calculate the spectral tilt of thermodynamic stringy fluctuations generated in the Hagedorn regime in this bouncing universe scenario. Generally we find a scale-invariant spectrum with a red tilt which is very small but does not vanish.