A trajectory-tracked, near-infrared autofluorescence imaging guided, biochemical signature-projected needle-type Raman spectroscopy (TNBN-RS) system integrated on a medical cart was developed for rapid wide-field breast tissue stratification. A wide-field (10 × 10 cm2) near-infrared autofluorescence (NIRAF) imaging subsystem was developed for gross stratification of breast tissue types based on higher NIRAF intensity associated with breast cancer, followed by projection of NIRAF-identified breast tumor margins onto the tissue of interest with a compact projector. Raman spectra were further acquired from the NIRAF projected regions for confirmed margin assessment using a needle-type Raman probe equipped with color camera-based probe trajectory tracking. The trajectory of the Raman probe and the accompanying RS biochemical signature-based margin assessment were instantly projected. A unique field of view (FOV) calibration method was proposed to calibrate the TNBN-RS FOVs, resulting in a projection accuracy of <2 mm. A graphical user interface (GUI) was developed in C# for system control, real-time processing and display of NIRAF images, Raman spectra, and projection of their results. The performance of the TNBN-RS system was validated on an ex vivo breast tissue, demonstrating its potential for rapid intraoperative breast tumor margin assessment.