Background and Objectives: Evaluation of the levels of cytokine and bone metabolic biomarkers (BMBs) in patients receiving fixed orthodontic therapy (FOT) and Invisalign. Materials and Methods: Sixty participants were enrolled after meeting the predefined inclusion criteria. Patients then underwent either FOT or Invisalign by allocating them randomly to each group (n = 30). The basic periodontal assessment was performed, including the plaque index (PI), gingival index (GI), and bleeding on probing (BoP), at baseline and again after 4 weeks. Gingival crevicular fluid (GCF) samples were taken from each individual at baseline and after 4 weeks. An enzyme-linked immunosorbent assay (ELISA) technique was used to determine the cytokine and BMB levels. An unpaired t-test compared the FOT and Invisalign group's means and SDs. Paired t-tests examined the difference between T0 baseline and T1. Results: Patients treated with either FOT or Invisalign presented no statistically significant difference in terms of periodontal parameters such as PI, GI, and BoP (p > 0.05). The levels of IL-6 were significantly higher in patients treated with FOT as compared to Invisalign at T1 (p < 0.05) The other tested cytokines, IL-10, 13, 17, and GM-CSF, were not significantly different in either the FOT or Invisalign group at baseline and 4 weeks follow-up (p > 0.05). Regarding BMBs, it was detected that NTx and OC levels in both of the investigated groups were not significantly different at baseline and after 4 weeks (p > 0.05). However, NTx levels rose significantly (p < 0.05) and OC levels fell from T0 to T1. Conclusions: FOT and Invisalign displayed comparable outcomes in terms of cytokine and BMB levels. However, only IL-6 and NTx were significantly different at week 4 from baseline.