Dr. K.C. Pani, a Food and Drug Administration medical officer, pleaded not guilty in Baltimore federal court yesterday to charges he accepted up to $48,200 in illegal gratuities from a nationally known advocate of a controversial drug he was responsible for regulating.

Pani's plea follows a similar profession of innocence Monday by Dr. Stanley Jacob, 57, an associate professor of surgery at the University of Oregon and the promoter of DMSO, a solvent traditionally used in industry and as an animal liniment. Pani, 63, is charged with accepting 24 payments from Jacob.

Both Jacob and Pani are free on personal bond pending their trial, scheduled for the week of Feb. 22 before U.S. District Court Judge Joseph H. Young. A pretrial hearing is set Feb. 1.

The Oregon doctor has promoted the drug as a pain reliever through congressional testimony and reportedly has used it in treating celebrities, including Olympic athletes, New York City Ballet stars and former Alabama Gov. George Wallace.

The FDA, acting on Pani's recommendation, approved the use of DMSO for treatment of bladder inflammation in 1978. A Salt Lake City firm in which Jacob owns stock provided one of two studies supporting the decision. According to the indictments, the checks in question were written between Dec. 1, 1975, and Jan. 6, 1979, during which time Pani was solely responsible for monitoring experimental uses of DMSO for the government.

Since the indictments last week, Pani has been on administrative leave from the agency. He continues to draw his $50,112 annual salary but is barred from reporting for work.