Contactin-associated protein 1 (CNTNAP1)-related congenital hypomyelinating neuropathy (CHN) is a rare type of peripheral neuropathy and has a clinically heterogeneous presentation. We report a neonate with an atypical presentation in the form of global hypotonia, facial diparesis and partial response to neostigmine challenge test. There was no clinical improvement on initiation of anticholinesterase drug for suspected congenital myasthenia and hence stopped. Detection of a pathogenic variant in CNTNAP1 gene by clinical exome sequencing and subsequent reverse phenotyping confirmed CHN as the aetiology for this floppy neonate, which is known to have high mortality. The baby was given supportive care and she succumbed secondary to complications of prolonged ventilation.