Selenium (Se) and zinc (Zn) are functional mineral elements that are beneficial to human health, and their contents in soil partly influence those in cultivated crops. To further characterize the content levels and spatial distribution of soil Se and Zn in the major agricultural areas east of the Sejila Mountains and to identify potential Se- and Zn-rich zones, this study analyzed total Se, total Zn, available Se, and available Zn in 92 farmland soil samples collected from nine townships of Bomi County, southeastern Xizang. Results showed that total Se, total Zn, available Se, and available Zn ranged from 0.000 to 1.426, 6.90 to 143.10, 0.001 to 0.114, and 0.078 to 8.540 mg/kg, respectively. Fifty-four samples (59%) reached the Se-enriched level for total Se, whereas only five samples (5%) reached that level for available Se, and 41% of the samples were at moderate level or above for available Se. Forty-eight percent of the samples had total Zn at moderate level or above, with a mean of 63.1 mg/kg, which was lower than the average of Xizang (73.7 mg/kg), and about half of the samples were at deficient or relatively deficient levels. About 71% of the samples (65/92) had available Zn at moderate level or above, indicating a relatively high content of available Zn. The contents of total Se, available Se, total Zn, and available Zn showed no distinct horizontal spatial pattern; total Se and available Zn increased significantly with altitude, available Se tended to increase but not significantly, and total Zn showed no clear altitudinal trend. In summary, the contents of total Se and available Zn were relatively high, total Zn was generally at a moderate-to-low level, and samples with Se-enriched available Se were scarce in farmland soils of the study area. Se- and Zn-rich farmlands in some areas deserve further tracking research to support the utilization of local soil resources and the development of functional agriculture.