Despite the growing interest in the use of probiotics in broilers as feed additives, studies conducted to investigate the effect of probiotic administration on acute phase responses and the impact on muscle growth parameters in broilers are still limited. In this study, we investigated the effect of Bacillus amyloliquefaciens CECT 5940 on relative gene expression for growth factors involved in muscle development (insulin-like growth factors, myogenic factor 5, paired-box transcription factor), percentage of proliferating antigen cell nuclei in breast muscle, and secretion of acute phase proteins (serum amyloid A, haptoglobin, alpha-acid glycoprotein) in the peripheral blood of broilers. Sixty one-day-old chicks from the experimental group were sprayed with a probiotic containing B. amyloliquefaciens at a dose of 1 × 10 CFU/g directly after hatching and received the probiotic in drinking water (50 × 10 CFU/1000 L) for 5 consecutive days of life. Sampling was performed on the 5th, 8th, and 12th day of life of the chicks. From the obtained results, we can conclude that B. amyloliquefaciens modulated the gene expression of selected growth parameters in the pectoral muscle, thereby increasing the number of satellite cells, however, their uptake into muscle fibers and thus increased hypertrophic growth was not proven at the time of the last sampling. At the same time, it demonstrated a potentiating effect on PCNA expression in chicken breast muscles in the early intensive growth phase of broiler chickens and modulated the production of acute phase proteins, which may contribute to improving adaptive processes during the growth and development of broilers.