Malinina began the 1998–1999 Grand Prix season with a 5th-place finish at the 1998 Skate America. Shortly afterward, in November 1998, Malinina and Skorniakov settled in Dale City, Virginia, drawn by better training conditions. In December, Malinina won her first Grand Prix title at the 1998 NHK Trophy and qualified for her first GPF Final. In February 1999, she competed at the inaugural Four Continents Championships and became its first ladies' gold medalist. The following month, she defeated both Maria Butyrskaya and Irina Slutskaya for the gold medal at the Grand Prix Final, held in Saint Petersburg. She finished her season by placing a career-best 4th at the World Championships.