Pharmacotherapy, also known as pharmacological therapy or drug therapy, is defined as medical treatment that utilizes one or more pharmaceutical drugs to improve ongoing symptoms (symptomatic relief), treat the underlying condition, or act as a prevention for other diseases (prophylaxis).

It can be distinguished from therapy using surgery (surgical therapy), radiation (radiation therapy), movement (physical therapy), or other modes. Among physicians, sometimes the term medical therapy refers specifically to pharmacotherapy as opposed to surgical or other therapy; for example, in oncology, medical oncology is thus distinguished from surgical oncology.

Today's pharmacological therapy has evolved from a long history of medication use, and it has changed most rapidly in the last century due to advancements in drug discovery. The therapy is administered and adjusted by healthcare professionals according to the evidence-based guidelines and the patient's health condition. Personalized medicine also plays a crucial role in pharmacological therapy. Personalized medicine, or precision medicine, takes account of the patient's genetic variation, liver function, kidney function, etc, to provide a tailor-made treatment for a patient. In pharmacological therapy, pharmacists will also consider medication compliance. Medication compliance, or medication adherence, is defined as the degree to which the patient follows the therapy that is recommended by the healthcare professionals.

The use of medicinal substances can be traced back to 4000 BC in the Sumer civilization. Healers at the time (called apothecaries), for example, understood the application of opium for pain relief. The history of natural remedies can also be found in other cultures, including traditional Chinese medicine in China and Ayurvedic medicine in India, which are still in use nowadays. Dioscorides, a 1st -century Greek surgeon, described more than six hundred animals, plants, and their derivatives in his medical botany, which remained the most influential pharmacopeia for fourteen hundred years. Besides substances derived from living organisms, metals, including copper, mercury, and antimony, were also used as medical therapies. They were said to cure various diseases during the late Renaissance. In 1657, tartar emetic, which is an antimony compound, was credited with curing Louis XIV of typhoid fever. The drug was also administered intravenously for the treatment of schistosomiasis in the 20th century. However, due to the concern over acute and chronic antimony poisoning, the role of tartar emetic as an antischistosomal agent was gradually replaced after the advent of praziquantel.

Other than using natural products, humans also learned to compound medicine by themselves. The first pharmaceutical text was found on clay tablets from the Mesopotamians, who lived around 2100 BC. Later in the 2nd century AD, compounding was formally introduced by Galen as "a process of mixing two or more medicines to meet the individual needs of a patient". Initially, compounding was only done by individual pharmacists, but in the post-World War II period, pharmaceutical manufacturers surged in number and took over the role of making medicine. Meanwhile, there was a marked increase in pharmaceutical research, which led to a growing number of new drugs. Most drug discovery milestones were made in the last hundred years, from antibiotics to biologics, contributing to the foundation of current pharmacological therapy.

Most drugs were discovered by empirical means, including observation, accident, and trial and error. One famous example is the discovery of penicillin, the first antibiotic in the world. The substance was discovered by Alexander Fleming in 1928 after a combination of unanticipated events occurred in his laboratory during his summer vacation. The Penicillium mold on the petri dish was believed to secrete a substance (later named "penicillin") that inhibited bacterial growth. Large pharmaceutical companies then started to establish their microbiological departments and search for new antibiotics. The screening program for antimicrobial compounds also led to the discovery of drugs with other pharmacological properties, such as immunosuppressants like Cyclosporin A.

The discovery of penicillin was a serendipitous (i.e. chance) discovery. Another, more advanced approach to drug discovery is rational drug design. The method is underpinned by an understanding of the biological targets of the drugs, including enzymes, receptors, and other proteins. In the late 19th century, Paul Ehrlich observed the selective affinity of dyes for different tissues and proposed the existence of chemoreceptors in our bodies. Receptors were believed to be the specific binding sites for drugs. The drug-receptor recognition was described as a key-and-lock interplay by Emil Fischer in the early 1890s. It was later found that the receptors can either be stimulated or inhibited by chemotherapeutic agents to attain the desired physiological response. Once the ligand interacting with the target macromolecule is identified, drug candidates can be designed and optimized based on the structure-activity relationship. Nowadays, artificial intelligence is employed in drug design to predict drug-protein interactions, drug activity, the 3D configuration of proteins, etc.

Evidence-based medicine is defined as deploying the best current scientific evidence that is available to give the best treatment and make the best decision effectively and efficiently. Clinical guidelines are developed based on scientific evidence; for example, the ACC/AHA guidelines (for cardiovascular diseases), the GOLD guidelines (for chronic obstructive pulmonary disease), the GINA guidelines (for asthma), etc. They convert and classify the evidence using a systematic method, aiming to provide care with quality. The guidelines cannot substitute clinical judgment, as they cannot meet all the circumstances. Healthcare professionals can use the clinical guidelines as references or evidence to support their clinical judgement when prescribing therapy to patients.