Surface‐enhanced Raman spectroscopy (SERS)‐based biosensors have attracted much attention for their label‐free detection, ultrahigh sensitivity, and unique molecular fingerprinting. In this study, a wafer‐scale, ultrasensitive, highly uniform, paper‐based, portable SERS detection platform featuring abundant and dense gold nanopearls with narrow gap distances, are prepared and deposited directly onto ultralow‐surface‐energy fluorosilane‐modified cellulose fibers through simple thermal evaporation by delicately manipulating the atom diffusion behavior. The as‐designed paper‐based SERS substrate exhibits an extremely high Raman enhancement factor (3.9 × 1011), detectability at sub‐femtomolar concentrations (single‐molecule level) and great signal reproductivity (relative standard deviation: 3.97%), even when operated with a portable 785‐nm Raman spectrometer. This system is used for fingerprinting identification of 12 diverse analytes, including clinical medicines (cefazolin, chloramphenicol, levetiracetam, nicotine), pesticides (thiram, paraquat, carbaryl, chlorpyrifos), environmental carcinogens (benzo[a]pyrene, benzo[g,h,i]perylene), and illegal drugs (methamphetamine, mephedrone). The lowest detection concentrations reach the sub‐ppb level, highlighted by a low of 16.2 ppq for nicotine. This system appears suitable for clinical applications in, for example, i) therapeutic drug monitoring for individualized medication adjustment and ii) ultra‐early diagnosis for pesticide intoxication. Accordingly, such scalable, portable and ultrasensitive fibrous SERS substrates open up new opportunities for practical on‐site detection in biofluid analysis, point‐of‐care diagnostics and precision medicine.