In 1998, the Florida Pharmacy Board received several complaints against Petmeds alleging that the company had issued medications without a prescription from a veterinarian. The complaint was settled in 1999 with the FPB requiring Petmeds to pay a small fine without admitting any wrongdoing. The complaints involved the referral of prescription requests to an "alternate veterinarian," who had never had any contact with the pet (but who reviewed the petís medical history) after the pets' treating veterinarian declined to issue a prescription without supplying a medical reason for the refusal, thereby ignoring the judgment of a veterinarian who had a valid veterinarian-client-patient relationship in favor of someone who had never seen the pet.
In 2002, Petmeds was charged by the Florida Pharmacy Board for "operating an 'alternate veterinarian program' that contracted with veterinarians to write prescriptions for animals they had never examined". PetMeds agreed to pay penalties and dismantle the program, plus serve three years of probation and community service. The company reached a similar agreement in Ohio, including five years' probation. In 2002, Petmeds was sued by the Texas State Board of Veterinary Medical Examiners for similar issues to the Florida case. The suit was settled without any admission of wrongdoing.
In 2001, Petmeds and the United States Environmental Protection Agency settled a "stop sales order" after Petmeds had sold flea control products that had been purchased outside of the United States and therefore gave their dosages in metric numbers. The maker of the misbranded product, Novartis, also sued Petmeds and other pharmacies over the issue.
In 2004, after the company went public, six securities lawsuits were brought against Petmeds by its shareholders, claiming that Petmeds had delayed disclosing past problems in order time to allow its executives, including founder Marc Puleo, to sell off their shares. PetMed always maintained that the suits were without merit and in 2005, all six suits were voluntarily dismissed by the plaintiffs