Paper-based surface-enhanced Raman scattering (SERS) sensors have garnered much attention in the past decade owing to their ubiquity, ease of fabrication, and environmentally friendly substrate. The main drawbacks of a paper substrate for a SERS sensor are its high porosity, inherent hygroscopic nature, and hydrophilic surface property, which reduce the sensitivity and reproducibility of the SERS sensor. Here, we propose a simple, quick, convenient, and economical method for hydrophilic to hydrophobic surface modification of paper, while enhancing its mechanical and moisture-resistant properties. The hydrophobic paper (h-paper) was obtained by spin-coating diluted polydimethylsiloxane (PDMS) solution onto the filter paper, resulting in h-paper with an increased contact angle of up to ≈130°. To complete the h-paper-based SERS substrate, gold nanoparticles arranged on graphene oxide (AuNPs@GO) were synthesized using UV photoreduction, followed by drop-casting of AuNPs@GO solution on the h-paper substrate. The enhancement of the SERS signal was then assessed by attaching a rhodamine 6G (R6G) molecule as a Raman probe material to the h-paper-based SERS substrate. The limit of detection was 10 nM with an R2 of 0.966. The presented SERS sensor was also tested to detect a thiram at the micromolar level. We expect that our proposed AuNPs@GO/h-paper-based SERS sensor could be applied to point-of-care diagnostics applications in daily life and in spacecraft.