Abstract: The etiology of side effects of antipsychotic medications can be conceptualized as involving both specific pharmacological actions of a drug and any mental and physical states attributed by the patient. Both factors are likely to be linked with neurocognitive functioning which may largely affect the subjective experience of side effects in patients with schizophrenia. In this study, we examined whether baseline neurocognitive functions, such as IQ, attention, executive functioning, and short-term memory, are associated with baseline and 6-month follow-up measures of self-reported Liverpool University Neuroleptics Side Effects Scale (LUNSERS) and clinician-rated Drug-Induced Extrapyramidal Symptoms Scale (DIEPSS). At the baseline, anxiety and depression were significantly associated with LUNSERS red herring (RH) and total side effects (SE) but not with DIEPSS. There was no association between LUNSERS and DIEPSS. Controlling for anxiety and depression, IQ was significantly correlated with DIEPSS, while choice reaction time (CRT) and stop signal task (SST) direction errors correlated with RH, and intra–extradimensional set-shifting (IED) total errors and pre-extradimensional set-shifting (pre-EDs) errors correlated with SE. The baseline SST direction errors further correlated significantly with RH and SE and DIEPSS total score of 6-month follow-up, and CRT mean and SD correct latency also correlated with DIEPSS. The correlations between the 6-month changes (Δ) in the same side effects measures and baseline neurocognitive measures were also significant, except that between RH and SST direction errors. Such evidences supported association between both self-rated and clinician-rated side effects and selective impairments in attention and executive functioning.