Chronic administration of zuclopenthixol (30 mg/kg/day for two years) in rats resulted in small, but significant, increases in the incidence of thyroid parafollicular carcinomas and, in females, of mammary adenocarcinomas and of pancreatic islet cell adenomas and carcinomas. An increase in the incidence of mammary adenocarcinomas is a common finding for D antagonists which increase prolactin secretion when administered to rats. An increase in the incidence of pancreatic islet cell tumours has been observed for some other D antagonists. The physiological differences between rats and humans with regard to prolactin make the clinical significance of these findings unclear. 
Withdrawal syndrome:  Abrupt cessation of therapy may cause acute withdrawal symptoms (eg, nausea, vomiting, or insomnia). Symptoms usually begin in 1 to 4 days of withdrawal and subside within 1 to 2 weeks.
Other permanent side effects are similar to many other typical antipsychotics, namely extrapyramidal symptoms as a result of dopamine blockade in subcortical areas of the brain. This may result in symptoms similar to those seen in Parkinson's disease and include a restlessness and inability to sit still known as akathisia, a slow tremor and stiffness of the limbs. Zuclopenthixol is thought to be more sedating than the related flupentixol, though possibly less likely to induce extrapyramidal symptoms than other typical depots. As with other dopamine antagonists, zuclopenthixol may sometimes elevate prolactin levels; this may occasionally result in amenorrhoea or galactorrhoea in severe cases. Neuroleptic malignant syndrome is a rare but potentially fatal side effect. Any unexpected deterioration in mental state with confusion and muscle stiffness should be seen by a physician.
Zuclopenthixol decanoate induces a transient dose-dependent sedation. However, if the patient is switched to maintenance treatment with zuclopenthixol decanoate from oral zuclopenthixol or from i.m. zuclopenthixol acetate the sedation will be no problem. Tolerance to the unspecific sedative effect develops rapidly.
;Very common Adverse Effects (≥10% incidence) 
* Dry Mouth
* Somnolence
* Akathisia
* Hyperkinesia
* Hypokinesia
;Common (1–10%) 
* Tachycardia
* Heart palpitations
* Vertigo
* Accommodation disorder
* Abnormal vision 
* Salivary hypersecretion
* Constipation
* Vomiting
* Dyspepsia
* Diarrhoea
* Asthenia
* Fatigue
* Malaise
* Pain (at the injection site)
* Increased appetite
* Weight gain
* Myalgia
* Tremor
* Dystonia
* Hypertonia
* Dizziness
* Headache
* Paraesthesia
* Disturbance in attention
* Amnesia
* Abnormal gait
* Insomnia
* Depression
* Anxiety
* Abnormal dreams
* Agitation
* Decreased libido 
* Nasal congestion
* Dyspnoea
* Hyperhidrosis
* Pruritus
;Uncommon (0.1–1%)
* Hyperacusis
* Tinnitus
* Mydriasis
* Abdominal pain
* Nausea
* Flatulence
* Thirst
* Injection site reaction
* Hypothermia
* Pyrexia
* Abnormal liver function tests
* Decreased appetite
* Weight loss
* Muscle rigidity
* Trismus
* Torticollis
* Tardive dyskinesia
* Hyperreflexia
* Dyskinesia
* Parkinsonism
* Syncope
* Ataxia
* Speech disorder
* Hypotonia
* Convulsion
* Migraine
* Apathy
* Nightmares
* Libido increased
* Confused state
* Ejaculation failure
* Erectile dysfunction
* Female orgasmic disorder
* Vulvovaginal
* Dryness
* Rash
* Photosensitivity
* Pigmentation disorder
* Seborrhoea
* Dermatitis
* Purpura
* Hypotension
* Hot flush
;Rare (0.01–0.1%)
* Thrombocytopenia
* Neutropenia
* Leukopenia
* Agranulocytosis
* QT prolongation
* Hyperprolactinaemia
* Hypersensitivity
* Anaphylactic reaction
* Hyperglycaemia
* Glucose tolerance impaired
* Hyperlipidaemia
* Gynaecomastia
* Galactorrhoea
* Amenorrhoea
* Priapism
* Withdrawal symptoms
;Very rare (<0.01%)
* Cholestatic hepatitis
* Jaundice
* Neuroleptic malignant syndrome
* Venous thromboembolism