Echinacea, a herbaceous, perennial flowering plant from the Compositae (Asteraceae) family, exhibits stimulating effects on myeloid progenitors (CFU-GMs) in rat bone marrow, as demonstrated in our previous study using a 75% (v v−1) ethanol extract of aerial parts. Expanding on this work, we have investigated eleven different Echinacea samples that belong to three species for their myeloid progenitor-stimulating activity. Simultaneously, we employed 1H-NMR spectroscopy (400 MHz, 0.02–10.02 ppm) and chemometric analysis to predict constituents responsible for activity. Female Sprague–Dawley rats received oral doses of ethanol extracts (0–200 mg extract dry weight kg−1 body weight) of Echinacea for seven days. Bone marrow cells were then cultured with CFU-GM growth factors. Extracts showing a statistically significant (p < 0.05) increase in CFU-GM, compared to the control, were considered active. Significant CFU-GM increases were observed in rats treated with seven Echinacea samples, ranging from 39% to 91% higher than the control, while four samples were inactive. All five Echinacea purpurea samples showed myeloid progenitor-stimulating activity, while one sample each of Echinacea angustifolia and Echinacea pallida also exhibited the same activity. By applying orthogonal partial least squares discriminant analysis (OPLS-DA) to the 1H-NMR spectra, we identified specific spectral bins (0.70–1.98 ppm aliphatic and 6.38–7.76 ppm aromatic) correlating with myelopoiesis stimulation. These findings highlight the potential of chemometric analysis using 1H-NMR spectroscopy to infer the chemical classes that could be responsible for the bioactive properties of complex herbal mixtures, like Echinacea.