The present invention provides methods, compositions, devices, and kits for treating cystinuria or related disorders, in which tiopronin is administered to a patient according to a modified- release strategy that releases tiopronin in critically-spaced, repeated pulses over time, to provide lower peak plasma levels but consistently higher urine levels of the drug for binding cystine. In particular, use of the present modified-release formulations and systems reduce side effects of tiopronin, thereby increasing patient compliance and quality of life, as well as achieving efficacy with less frequent administrations and/or lower total dosages.