Born on 11 September 1976 in Chennai, Tamil Nadu, Murali Kartik wanted to be a genetic engineer. He was a medium pacer in his early years, before switching to a left arm finger spinner in the classical mould, Kartik grew up trying to emulate past Indian orthodox spinners Bishen Singh Bedi, Maninder Singh and Venkatapathy Raju. He also garnered attention for what was perceived to be a fiery attitude, but took pride in coach Kapil Dev saying of him "I have never seen a player with such an attitude towards the game in my 20 years of international cricket".
Kartik started out in the junior system at Delhi. He broke into their Under-16 team in December 1992, and took a match total of 10/74 on debut against Himachal Pradesh, as well as scoring 52 not out in an innings victory. He took 2/91 in the next match against Haryana, but could no longer play in the Under-16s because of his advancing age. He could not break into the Under-19s at Delhi, and played no further youth domestic matches for two years, when he transferred to Railways and broke into their Under-19 team.
In five matches for his new team during the 1994–95, he took 24 wickets at 14.58 including a haul of 5/28 against Vidarbha. He was rewarded with selection in the Under-19 Central Zone team for the zonal one-day tournament, taking five wickets at 25.00 in four matches. He had little success with the bat, scoring 47 on one occasion during the season, but otherwise only aggregating nine runs in six innings.
The following season in 1995–96, Kartik had a more successful season for Railways Under-19s. He started with 5/73 and 5/55 against Madhya Pradesh and made it three five-wicket hauls in a row with 5/42 against Vidarbha. He took another five-wicket haul later in the season against Rajasthan and ended the competition with 38 wickets at 18.94 in seven matches. Railways made the final, where they faced Punjab. Kartik was Railways' most effective bowler, taking 4/57 in Punjab's first innings of 310. He then made 14 not out as Railways ceded a first innings lead, which was enough to give Punjab the title as the match ended in a draw. Kartik took 3/138 in the second innings. After the final, newly crowned champions took on the Rest of India, and Kartik took 2/25 and 4/89 to help his team to a six-wicket victory. Kartik had a less successful time in the zonal one-dayers for Central, taking only one wicket in three matches. He also improved his batting marginally, scoring 57 and three other double-digit scores.
As a result of his performances during the season, Kartik was called up to the Indian Under-19 team for an international series against their counterparts from South Africa. In the youth Test, he took 4/40 as India dismissed South Africa for 159 to take a 19-run lead. In the second innings, he took 3/30 as South Africa fell for 107 in pursuit of 277. In two youth one-day internationals that followed, Kartik was prominent in the Indian victories, taking 3/23 and 3/33 respectively.