A search for long-lived particles decaying into jets is presented. Data were collected with the CMS detector at the LHC from proton-proton collisions at a center-of-mass energy of 13 TeV in 2016, corresponding to an integrated luminosity of 35.9  fb−1. The search examines the distinctive topology of displaced tracks and secondary vertices. The selected events are found to be consistent with standard model predictions. For a simplified model in which long-lived neutral particles are pair produced and decay to two jets, pair production cross sections larger than 0.2 fb are excluded at 95% confidence level for a long-lived particle mass larger than 1000 GeV and proper decay lengths between 3 and 130 mm. Several supersymmetry models with gauge-mediated supersymmetry breaking or R-parity violation, where pair-produced long-lived gluinos or top squarks decay to several final-state topologies containing displaced jets, are also tested. For these models, in the mass ranges above 200 GeV, gluino masses up to 2300–2400 GeV and top squark masses up to 1350–1600 GeV are excluded for proper decay lengths approximately between 10 and 100 mm. These are the most restrictive limits to date on these models.