Lumbar degenerative disc disease (LDDD) is widely acknowledged as a significant contributor to low back pain (LBP), which is a prevalent and debilitating health condition affecting millions of individuals worldwide. The pathogenesis of LDDD and associated pain mechanisms are thought to be mediated by inflammatory mediators. Autologous conditioned serum (ACS, Orthokine) may be used for symptomatic treatment of LBP due to LDDD. This study aimed to compare the analgesic efficacy and safety of two routes of ACS administration, perineural (periarticular) and epidural (interlaminar), in the conservative treatment of LBP. This study used an open-label, randomized, controlled trial protocol. A group of 100 patients were enrolled in the study and randomly allocated into two comparative groups. Group A (n= 50) received the epidural (interlaminar) approach—2 ultrasound-guided injections as control intervention (each containing two doses of ACS—8 mL). Group B (n= 50) received the perineural (periarticular) approach—2 ultrasound-guided injections as experimental intervention at 7-day intervals (the same volume of ACS). Assessments consisted of an initial assessment (IA) and control assessments at 4 (T1), 12 (T2), and 24 (T3) weeks after the last intervention. Primary outcomes comprised Numeric Rating Scale (NRS), Oswestry Disability Index (ODI), Roland Morris Questionnaire (RMQ), and Euro Quality of Life—5 Dimensions–5 Levels (EQ-5D-5L): Index, Visual Analogue Scale (VAS), and Level Sum Score (LSS). Secondary outcomes included differences between groups in specific endpoints for the above-mentioned questionnaires. In conclusion, this study revealed that both perineural (periarticular) and epidural ACS injections tended to perform in a very similar way. Both routes of Orthokine application show significant improvement in the primary clinical parameters, such as pain and disability, and therefore, both methods can be considered equally effective in managing LBP due to LDDD.