Measuring the total charm cross section is important for the comparison to theoretical predictions of the highest precision available for charm today, which are completely known up to NNLO QCD for the total inclusive cross sections. These are also independent of charm fragmentation, while practical measurements of charm hadrons in a fiducial phase space are not. Recently the LHC experiments have reported non-universality of charm fragmentation, which shows that e.g. charm baryon-to-meson ratios are not universal in different collision systems, and that the related production fractions also depend on transverse momentum. This breaks the charm fragmentation universality that was assumed until recently for the extrapolation of experimental measurements to the full total charm cross section phase space. A proposal is made how to address this non-universality in a data driven way without the need to implement any particular non-universal fragmentation model. As a practical example, this method is applied to the extrapolation of published LHC measurements of $D^0$ production at $\sqrt{s}=5$ TeV to the corresponding total charm cross section, which fully accounts for charm fragmentation non-universality for the first time. The result, $8.43 ^{+1.05}_{-1.16}(\text{total})$ mb, differs substantially from the one assuming charm fragmentation universality, but still compares well to theoretical QCD predictions up to NNLO.