Krachunov started playing football with Maritsa Plovdiv. He made his first-team debut on 18 August 2007, at 18 years, in a 0–3 away defeat to Kaliakra Kavarna and quickly became a regular starter of the team, as a centre back. His first goal came on 11 May 2008, in a 3–1 home win over Minyor Radnevo. During his first two seasons, he earned 50 appearances in the East B PFG, but Maritsa were relegated at the end of the 2008–09 season. After one season, playing for Maritsa in third league, he joined Lokomotiv Plovdiv.
After a short trial, on 6 July 2010, Krachunov signed a three-year contract with Lokomotiv. He made his A PFG debut in a 2–2 draw against Litex Lovech on 22 August, coming on as a substitute for Youness Bengelloun. Krachunov netted Lokomotiv's only goal in their Bulgarian Cup loss, a 2–1 defeat at Pirin Blagoevgrad on 6 April 2011. Four days later, he scored his first league goal for Lokomotiv, in a 1–1 draw against Montana.
On 15 August 2011, reports linked Krachunov with a move to CSKA Sofia, adding depth to the position one day after Apostol Popov was lost for the season because of a knee injury. The following day, he completed his move to CSKA, on a three-year contract. He was handed the number 66 shirt.
He made his debut on 21 August, appearing as a substitute in a 2–1 win over Kaliakra Kavarna, and made his first start for the club in the following game against Montana. On 26 September, he scored his first goal for CSKA, scoring a header in CSKA's 4–1 league win over Vidima-Rakovski from a Spas Delev corner-kick. Krachunov then scored on 3 December in a Bulgarian Cup game against Spartak Pleven. On 15 March 2014, Krachunov scored a last-minute goal in the 1:0 win over Levski Sofia in an A PFG match. He joined Slavia Sofia in the summer of 2015, remaining with the "whites" until January 2016.
On 22 February 2016, Krachunov signed a contract with Scottish Premiership side St Johnstone, after a successful trial period with the club.
On 5 July 2017 he signed a contract with Sandecja Nowy Sącz.
In October 2011, Krachunov earned his first call-up to the Bulgaria national side for a friendly match against Ukraine and a Euro 2012 qualifier against Wales.
All stats correct as of 22 February 2016.
His brother Stefan Krachunov is also footballer.