We report the detection of a thick disk in the edge-on, low surface brightness (LSB), late-type spiral ESO 342-G017, based on ultra-deep images in the V and R bands obtained with the VLT Test Camera during Science Verification on UT1. All steps in the reduction procedure are fully described, which, together with an extensive analysis of systematic and statistic uncertainties, has resulted in surface brightness photometry that is reliable for the detection of faint extended structure to a level of V = 27.5 and R = 28.5 mag/square arcsec. The faint light apparent in these deep images is well-modeled by a thick exponential disk with an intrinsic scale height about 2.5 times that of the thin disk, and a comparable or somewhat larger scale length. Deprojection including the effects of inclination and convolution with the PSF allow us to estimate that the thick disk contributes 20-40% of the total (old) stellar disk luminosity of ESO 342-G017. To our knowledge, this is the first detection of a thick disk in an LSB galaxy, which are generally thought to be rather unevolved compared to higher surface brightness galaxies.