Absorption features in stellar atmospheres are often used to calibrate photocentric velocities for the kinematic analysis of further spectral lines. The Li feature at ∼6708 Å is commonly used, especially in the case of young stellar objects, for which it is one of the strongest absorption lines. However, this complex line comprises two isotope fine-structure doublets. We empirically measured the wavelength of this Li feature in a sample of young stars from the PENELLOPE/VLT programme (using X-shooter, UVES, and ESPRESSO data) as well as HARPS data. For 51 targets, we fit 314 individual spectra using the STAR-MELT package, resulting in 241 accurately fitted Li features given the automated goodness-of-fit threshold. We find the mean air wavelength to be 6707.856 Å, with a standard error of 0.002 Å (0.09 km s−1), and a weighted standard deviation of 0.026 Å (1.16 km s−1). The observed spread in measured positions spans 0.145 Å, or 6.5 km s−1, which is higher by up to a factor of six than the typically reported velocity errors for high-resolution studies. We also find a correlation between the effective temperature of the star and the wavelength of the central absorption. We discuss that exclusively using this Li feature as a reference for photocentric velocity in young stars might introduce a systematic positive offset in wavelength to measurements of further spectral lines. If outflow tracing forbidden lines, such as [O I] 6300 Å, is more blueshifted than previously thought, this then favours a disc wind as the origin for this emission in young stars.