Although the mechanism of DNA methylation‐mediated gene silencing is extensively studied, relatively little is known about how promoter methylated genes are protected from transcriptional silencing. SUVH1, an Arabidopsis Su(var)3‐9 homolog, was previously shown to be required for the expression of a few promoter methylated genes. By chromatin immunoprecipitation combined with sequencing, we demonstrate that SUVH1 binds to methylated genomic loci targeted by RNA‐directed DNA methylation. SUVH1 and its homolog SUVH3 function partially redundantly and interact with three DNAJ domain‐containing homologs, SDJ1, SDJ2, and SDJ3, thus forming a complex which we named SUVH‐SDJ. The SUVH‐SDJ complex components are co‐localized in a large number of methylated promoters and are required for the expression of a subset of promoter methylated genes. We demonstrate that the SUVH‐SDJ complex components have transcriptional activation activity. SUVH1 and SUVH3 function synergistically with SDJ1, SDJ2, and SDJ3 and are required for plant viability. This study reveals how the SUVH‐SDJ complex protects promoter methylated genes from transcriptional silencing and suggests that the transcriptional activation of promoter methylated genes mediated by the SUVH‐SDJ complex may play a critical role in plant growth and development. DNA methylation within promoters typically leads to transcriptional silencing. But little is known about how genes with methylated promoters are protected from transcriptional silencing. This study identifies a protein complex which binds to methylated promoters and is required for transcriptional activation.