In a typical X-ray imaging, an image is formed based on X-ray beam attenuation. The most common form of X-ray imaging is computed tomography (CT) which allows us to view the internal structure of tissues with fine detail. However, CT imaging provides little information about the functional capabilities of the tissues. In this dissertation, functional X-ray imaging modalities including time domain X-ray luminescence computed tomography (XLCT) and X-ray fluorescence computed tomography (XFCT) are explored for preclinical applications. The dose concerns related with these two imaging modalities are also investigated. Optical contrast agents may be injected into the subject to give more information of the tissue function for a more accurate diagnosis. These contrast agents can release optical photons when excited with X-rays while in proximity to chemical concentrations of interest in tissues. Cancerous tumors exhibit an acidic environment and are highly vascularized which increase oxygenation levels. Optical contrast agents can be made sensitive to the cancer pH change or oxygen levels and release light when excited by X-rays. This form of X-ray imaging is XLCT imaging. Usually, researchers tend to use the optical light intensity (light yield) from the contrast agent to create the image. However, the time information of the optical photon intensity (lifetime) is useful since the time measurements can detect microenvironmental changes that are unobservable by light yield measurements. The feasibility of using the lifetime of the contrast agent instead of the light yield to create the image was numerically explored. The findings of this work reported that the lifetime images were more accurate than light yield images. The lifetime images were also found to be independent of some typical imaging acquisition parameters. The use of X-rays to excite contrast agents that release secondary X-rays which are specific to the contrast agent material composition was also studied. This form of X-ray imaging is XFCT imaging. Chemotherapeutic drugs can be monitored in the body using this type of imaging without additional contrast agents being injected into the subject. By using a fine X-ray pencil beam and a ring detector, contrast agents embedded in an object were resolved with high contrast and submillimeter resolution with fewer imaging acquisitions. CT imaging traditionally uses cone or fan X-ray beam geometries to reduce the radiation dose and imaging time while providing quality images. The radiation safety concerns of using a fine X-ray pencil beam imaging for high resolution imaging was investigated. Typically, the radiation dose of pencil beam X-ray imaging is difficult to measure due to instrumentation limitations. Therefore, it is best to calculate the dose with Monte Carlo methods. X-ray imaging like XLCT benefit most from high resolution imaging to resolve sub millimeter targets in tissues. Results shows that if bright X-ray sources are used for the imaging scan, the radiation safety concerns with X-ray pencil beam imaging can be reduced and investigated further. The image quality of X-ray imaging relies heavily on the X-ray output number which is dependent on the X-ray tube current and the exposure time. A limiting factor of good image quality is the radiation dose that will be delivered to the imaging object. Conventional methods to estimate the dose are limited and/or standardized to a specific imaging object size and imaging protocol. To accurately estimate the dose in any imaging protocol, it is better to simulate the X-ray imaging with a Monte Carlo platform. Among Monte Carlo platforms, GATE (Geant4 Application for Tomographic Emission) has gained traction in medical imaging applications. So far, there is no good way to setup the photon number for a desired X-ray tube current in GATE. The findings of this work provide an approach to correlate the X-ray tube current exposure time (mAs) to the X-ray photon number in the GATE simulation of the X-ray tube. The work provides a method to accurately estimate the dose in an imaging protocol. The work presented in this dissertation is meant to showcase the feasibility of novel imaging techniques to promote advancements in functional X-ray imaging.