Purpose Dual-energy (DE) x-ray imaging has many clinical applications in radiography, fluoroscopy, and CT. This work characterizes a prototype dual-layer (DL) flat-panel detector (FPD) and investigates its DE imaging capabilities for applications in two-dimensional (2D) radiography/fluoroscopy and quantitative three-dimensional (3D) cone-beam CT. Unlike other DE methods like kV switching, a DL FPD obtains DE images from a single exposure, making it robust against patient and system motion. Methods The DL FPD consists of a top layer with a 200 µm-thick CsI scintillator coupled to an amorphous silicon (aSi) FPD of 150 µm pixel size and a bottom layer with a 550 µm thick CsI scintillator coupled to an identical aSi FPD. The two layers are separated by a 1-mm Cu filter to increase spectral separation. Images (43 × 43 cm2 active area) can be readout in 2 × 2 binning mode (300 µm pixels) at up to 15 frames per second. Detector performance was first characterized by measuring the MTF, NPS, and DQE for the top and bottom layers. For 2D applications, a qualitative study was conducted using an anthropomorphic thorax phantom containing a porcine heart with barium-filled coronary arteries (similar to iodine). Additionally, fluoroscopic lung tumor tracking was investigated by superimposing a moving tumor phantom on the thorax phantom. Tracking accuracies of single-energy (SE) and DE fluoroscopy were compared against the ground truth motion of the tumor. For 3D quantitative imaging, a phantom containing water, iodine, and calcium inserts was used to evaluate overall DE material decomposition capabilities. Virtual monoenergetic (VM) images ranging from 40 to 100 keV were generated, and the optimal VM image energy which achieved the highest image uniformity and maximum contrast-to-noise ratio (CNR) was determined. Results The spatial resolution of the top layer was substantially higher than that of the bottom layer (top layer 50% MTF = 2.2 mm-1 , bottom layer = 1.2 mm-1 ). A substantial increase in NNPS and reduction in DQE were observed for the bottom layer mainly due to photon loss within the top layer and Cu filter. For 2D radiographic and fluoroscopic applications, the DL FPD was capable of generating high-quality material-specific images separating soft tissue from bone and barium. For lung tumor tracking, DE fluoroscopy yielded more accurate results than SE fluoroscopy, with an average reduction in the root mean square error (RMSE) of over 10×. For the DE-CBCT studies, accurate basis material decompositions were obtained. The estimated material densities were 294.68 ± 17.41 and 92.14 ± 15.61 mg/ml for the 300 and 100 mg/ml calcium inserts, respectively, and 8.93 ± 1.45, 4.72 ± 1.44, and 2.11 ± 1.32 mg/ml for the 10, 5, and 2 mg/ml iodine inserts, respectively, with an average error of less than 5%. The optimal VM image energy was found to be 60 keV. Conclusions We characterized a prototype DL FPD and demonstrated its ability to perform accurate single-exposure DE radiography/fluoroscopy and DE-CBCT. The merits of the DL detector approach include superior spatial and temporal registration between its constituent images, and less complicated acquisition sequences.