The jackknife method gives an internal covariance estimate for large-scale structure surveys and allows model-independent errors on cosmological parameters. Using the SDSS-III BOSS CMASS sample, we study how the jackknife size and number of resamplings impact the precision of the covariance estimate on the correlation function multipoles and the error on the inferred baryon acoustic scale. We compare the measurement with the MultiDark Patchy mock galaxy catalogues, and we also validate it against a set of lognormal mocks with the same survey geometry. We build several jackknife configurations that vary in size and number of resamplings. We introduce the Hartlap factor in the covariance estimate that depends on the number of jackknife resamplings. We also find that it is useful to apply the tapering scheme to estimate the precision matrix from a limited number of resamplings. The results from CMASS and mock catalogues show that the error estimate of the baryon acoustic scale does not depend on the jackknife scale. For the shift parameter a, we find an average error of 1.6 per cent, 2.2 per cent and 1.2 per cent, respectively, from CMASS, Patchy, and lognormal jackknife covariances. Despite these uncertainties fluctuate significantly due to some structural limitations of the jackknife method, our a estimates are in reasonable agreement with published pre-reconstruction analyses. Jackknife methods will provide valuable and complementary covariance estimates for future large-scale structure surveys.