The Khokji script is written using thirty-six consonant letters, eight vowel letters, and eight vowel diacritics. Consonant letters contain a consonant followed by an inherent [a] vowel. Vowel diacritics can be added to a consonant letter to change the [a] vowel into something else. For example, the letter ka + the vowel diacritic e represents the sound [ke]. Vowel letters are used for writing vowels which are not preceded by a consonant, i.e. those which are preceded by another vowel, or which are at the start of a word.

There is a discrepancy as to which sounds are represented by vowel letters, and which are represented by vowel diacritics. Spoken Sindhi distinguishes between long and short vowels. However, only the short [a] and long [a:] are represented by short and long vowel letters, and only the short [i] and long [i:] are represented by short and long vowel diacritics. The other letters and diacritics are used to represent both short and long variants of their respective vowels. This is unusual among Brahmic scripts, which tend to consistently represent vowel length in writing.