To investigate new genetic etiologies of Rett syndrome (RTT) or RTT-like syndrome, targeted next-generation sequencing (NGS) was performed on 44 Chinese patients with RTT (-like) syndrome, in whom genetic analysis of MECP2, CDKL5 and FOXG1 was negative. The mutation rate was 31.8% (14/44). Among the subjects, a de novo mutation (c.275_276ins AA, p.Cys92*) in KIF1A was identified in a girl with all core features of typical RTT. A patient with early seizure variant of RTT were discovered having GRIN1 gene mutation (c.2337C>A, p.Val793Phe). Additionally, a compound heterozygous PPT1 gene mutation was detected in a girl, who initially displayed typical RTT features, but progressed into neuronal ceroid lipofuscinoses (NCL) afterwards. Mutations in KCNQ2, MEF2C, WDR45, TCF4, IQSEC2 and SDHA were also found in this study. Notably, it is the first time that mutations in GRIN1 and KIF1A were linked to RTT (-like) profiles. Our findings expand the genetic heterogeneity of RTT (-like) phenotypes, and also suggest that some patients with inherited metabolic disease such as NCL, might displayed RTT features initially.