Cochlear implants (CIs) restore functional hearing in persons with a severe hearing impairment. Despite being one of the most successful bionic prosthesis, performance with CI (in particular speech understanding in noise) varies considerably across its users. The ability of the auditory pathway to encode temporal envelope modulations (TEMs) and the effect of degenerative processes associated with hearing loss on TEM encoding is assumed to be one of the reasons underlying the large intersubject differences in CI performance. The objective of the present study was to investigate how TEM encoding of the stimulated neural ensembles of human CI recipients is related to speech perception in noise (SPIN). We used electroencephalography as a noninvasive electrophysiological measure to assess TEM encoding in the auditory pathway of CI users by means of the 40-Hz electrically evoked auditory steady state response (EASSR). Nine CI users with a wide range of SPIN outcome were included in the present study. TEM encoding was assessed for each stimulation electrode of each subject and new metrics; the CI neural modulation transmission difference (CIMTD) and the CI neural modulation transmission index (CIMTI) were developed to quantify the amount of variability in TEM encoding across the stimulated neural ensembles of the CI electrode array. EASSR patterns varied across the CI electrode array and subjects. We found a strong correlation (r = 0.89, p = 0.001) between the SPIN outcomes and the variability in EASSR amplitudes across the array as assessed with CIMTD/CIMTI. The results of the present study show that the 40-Hz EASSR can be used to objectively assess the neural encoding of TEMs in human CI recipients. Overall reduced or largely variable TEM encoding of the neural ensembles across the electrode array, as quantified with the CIMTD/CIMTI, is highly correlated with speech perception in noise outcome with a CI.