The paucity of studies on permafrost runoff generation processes, especially in mountain permafrost, constrains the understanding of permafrost hydrology and prediction of hydrological responses to permafrost degradation. This study investigated runoff generation processes, in addition to the contribution of summer thaw depth, soil temperature, soil moisture, and precipitation to streamflow in a small upland permafrost basin in the northern Tibetan Plateau. Results indicated that the thawing period and the duration of the zero-curtain were longer in permafrost of the northern Tibetan Plateau than in the Arctic. Limited snowmelt delayed the initiation of surface runoff in the peat permafrost in the study area. The runoff displayed intermittent generation, with the duration of most runoff events lasting less than 24 h. Precipitation without runoff generation was generally correlated with lower soil moisture conditions. Combined analysis suggested runoff generation in this region was controlled by soil temperature, thaw depth, precipitation frequency and amount, and antecedent soil moisture. This study serves as an important baseline to evaluate future environmental changes on the Tibetan Plateau.