Is working in a pharma company that makes alcohol-based medicine haram?

The prohibition in the Quran addresses khamr - intoxicating drink - and the stated reason is intoxication and its consequences. Ethanol in a medicine is not consumed as a drink, is present in a quantity that does not intoxicate, and serves a technical function as a solvent or preservative. Most scholars therefore apply the principle that a substance transformed within a preparation, in a quantity that cannot intoxicate, does not carry the ruling of the intoxicating beverage.

Yes, and these are the clearest cases. Hand sanitiser is applied externally and not consumed at all, and alcohol used as a preservative or solvent in a vaccine is present in trace amounts serving a technical purpose. Both received broad scholarly acceptance, and the question was addressed directly and widely during the recent period of mass vaccination and heightened hygiene practice.

This raises a separate concern from alcohol, and scholars differ more here. Many apply the same transformation reasoning - the gelatin has been chemically altered from its original substance - and permit it, particularly where a medical need exists and no alternative is available. Others hold that the transformation is insufficient. Bovine and plant-derived capsules are increasingly available, and preferring them where a choice exists is the cautious position.