Background/Objectives: Aging is associated with declines in cognitive function and neurotrophic support. Brain-derived neurotrophic factor (BDNF) and insulin-like growth factor-1 (IGF-1) are peripheral biomarkers discussed in relation to brain health and aging. This study investigated changes in serum BDNF, IGF-1, and cognitive screening scores after a 16-week Hatha Yoga program performed twice or four times per week in older women. Methods: Fifty-one community-dwelling women aged 70–79 years were allocated to a twice-per-week yoga group (2YG; n = 17), a four-times-per-week yoga group (4YG; n = 17), or a non-exercise control group (CON; n = 17) based on availability and participant preference; forty-three participants completed the study. Serum BDNF and IGF-1 were analyzed using enzyme-linked immunosorbent assay and chemiluminescent immunoassay, and cognitive status was evaluated using the Cognitive Impairment Screening Test (CIST). Outcomes were analyzed using two-way repeated-measures ANOVA and additional ANCOVA models adjusting for corresponding baseline values. Exploratory correlations were examined between biomarker changes and CIST changes. Effect sizes and 95% confidence intervals were reported. Results: BDNF showed a significant main effect of time (p < 0.05) without a significant group × time interaction; ANCOVA adjusting for baseline BDNF showed no significant group effect (p = 0.270). IGF-1 showed a significant group × time interaction (p < 0.01) with increases in both yoga groups; ANCOVA adjusting for baseline IGF-1 showed a significant group effect (p = 0.001). CIST showed a significant main effect of time (p < 0.01), but changes were small and the group × time interaction was not significant; ANCOVA adjusting for baseline CIST showed no significant group effect (p = 0.114). Biomarker changes were not clearly correlated with CIST changes (ΔBDNF–ΔCIST: r = −0.244, p = 0.115; ΔIGF-1–ΔCIST: r = −0.050, p = 0.750). Conclusions: In this quasi-experimental study with non-random allocation and limited covariate information, changes in peripheral neurotrophic factors and only small changes in cognitive screening scores were observed after participation in a 16-week Hatha Yoga program. However, frequency-dependent conclusions are limited, and findings should be interpreted cautiously as screening-level, hypothesis-generating reference data. Nevertheless, the program is considered a feasible, low-risk health promotion activity for older women and may inform future randomized or well-controlled studies.