Mehbooba also lauded the performance of all those who cracked the country's premier civil services examination from the state, an official spokesman said.
Admiring Khan for his success, she said his feat will inspire many other youngsters.
"There is no dearth of talent in our state which Khan has proved today.Many congratulations for having successfully cleared the examinations with flying colours and my best wishes as you start your journey to serve the people," she said.
"Heartiest congratulations to Aamir ul Shafi Khan of Devipora, Anantnag for standing second in the UPSC exams this year. Well done young man," Omar tweeted.
Omar, also the opposition National Conference (NC) working president, wrote "May your star shine bright & may you bring laurels to your family, your state & your country. All the very best for a bright future Aamir.