Apparently, “apothecary” refers to the individual, not the establishment. So, the difference between an apothecary and a pharmacist? It looks like what used to be a single role of apothecary has now splintered into many roles, with what remains now being indistinguishable from a pharmacist.
Though, in some parts of the world, the labels are used interchangeably, the apothecary used to be a type of pharmacist who not only distributed medications to both patients and professionals, but also dispensed general medical advice, provided other services (such as [some] actual surgeries) and might have also sold tobacco (Apothecary):
Apothecary /əˈpɒθᵻkəri/ is one term for a medical professional who formulates and dispenses materia medica to physicians, surgeons and patients. The modern pharmacist (also colloquially referred to as a chemist in British English) has taken over this role and in some languages and regions the word is still used to refer to a retail pharmacy or a pharmacist who owns one. The apothecaries’ investigation of herbal and chemical ingredients was a precursor to the modern sciences of chemistry and pharmacology.
In addition to dispensing medicines, the apothecary offered general medical advice and a range of services that are now performed by other specialist practitioners, such as surgeons and obstetricians. Apothecaries often operated through a retail shop which, in addition to ingredients for medicines, sold tobacco and patent medicines.