Synonymous codons are used in different frequencies in genomes, the phenomenon that is known as codon usage bias. It has been extensively reported that the codon usage bias is strongly correlated to mRNA level, a phenomenon that is frequently explained by natural selection on translational accuracy and/or efficiency. That is, reduced translational accuracy and efficiency leads to cellular toxicity and ribosome sequestering, respectively, and such impact scales with gene expression level, which leads to stronger natural selection on synonymous codon usage among highly expressed genes. In sharp contrast, the potential role of codon usage bias in regulating mRNA level has been ignored for long, although it could explain the correlation between mRNA level and codon usage bias as well. Here, we directly measured the impact of synonymous mutations on mRNA level, by generating in total 3,556 synonymous variants of the gene encoding green fluorescent protein (GFP), inducing their expression from the genome of the budding yeast, and measuring their mRNA levels with high-throughput sequencing. Surprisingly, we found that preferred codons up-regulate mRNA levels in general. In other words, even if natural selection on translation is not operating, a strong correlation between codon usage bias and mRNA level could be observed in genomes. Our study reveals the vital role of codon usage bias in regulating mRNA level, provides an alternative explanation for the well-known correlation between codon usage bias and mRNA level, and calls for re-evaluation of theories on the evolution of codon usage bias.