miRNAs, a class of non-coding single-stranded small RNAs with regulatory roles, play an important part in the regulation of biological rhythms. In order to explore the spatio-temporal expression characteristics of miR-21, as well as the effects of fasting on its expression, real-time fluorescence quantitative PCR was used to analyze the expression of miR-21 in the embryos of different developmental stages and tissues of the Chinese perch Siniperca chuatsi, as well as the rhythmic expression after 5 d of fasting. The results showed that a high level of miR-21 can be detected in the early stage of embryonic development, expression of miR-21 decreases as the embryo develope, and only a small amount of miR-21 could be detected in the early gastrula stage. The expression of miR-21 increased after the gastrula stage, but there was no significant difference in the expression of miR-21 after the neurula stage, except in the tail-bud and heart-beating stages. miR-21 was expressed in all tested tissues, with high levels of expression in heart, intestine, and red muscle. Under normal feeding, miR-21 expression in Chinese perch muscle showed a circadian rhythm: low in the day and high in the night. After 5 d of fasting, expression of miR-21 was still in a circadian rhythm, but its median value, oscillation amplitude, and peak phase were significantly affected. Target gene prediction analysis showed that the 3′UTR sequence of Arntl2 mRNA had miR-21 binding sites. Taken together, results indicated that the expression of miR-21 in the embryo was maternal and began to rise after the neurula stage, suggesting that miR-21 plays an important role in embryonic organogenesis after this stage. The expression of miR-21 was not tissue-specific, but it may play an important role in the growth and development of heart, intestine, and red muscle. Fasting stress could affect the circadian rhythm of miR-21 in Chinese perch muscle, and miR-21 might be involved in the regulation of the rhythm of the Chinese perch by regulating the circadian gene Arntl2, thus affecting muscle growth and physiological functions.