Surface-enhanced Raman scattering has developed into a mature analytical technique useful in various applications; however, the reproducible fabrication of a portable SERS substrate with high sensitivity and good uniformity is still an ongoing pursuit. Reported herein is a rapid fabrication method of an inexpensive SERS substrate that enables sub-nanomolar detection of molecular analytes. The SERS substrate is obtained by application of silver nanoparticles (Ag NPs)-based ink in precisely design patterns with the aid of an in-house assembled printer equipped with a user-fillable pen. Finite-difference time-domain (FDTD) simulations show a 155-times Ag NP electric field enhancement for Ag nanoparticle pairs with particle spacing of 2 nm. By comparing the SERS performance of SERS substrate made with different support matrices and fabrication methods, the PET-printed substrate shows optimal performance, with an estimated sensitivity enhancement factor of 107. The quantitative analysis of rhodamine 6G absorbed on optimized SERS substrate exhibits a good linear relationship, with a correlation coefficient (R2) of 0.9998, between the SERS intensity at 610 cm−1 and the concentration in the range of 0.1 nM—1μM. The practical low limit detection of R6G is 10 pM. The optimized SERS substrates show good stability (at least one month) and have been effectively tested in the detection of cancer drugs, including doxorubicin and metvan.