Chalkias started his career in the Panathinaikos youth academy in the 96/96 double winning PAO team and was loaned out for his first two seasons to Apollon Athens. After he returned, he was forced to play third keeper to the legendary Jozef Wandzik and greek legend Antonis Nikopolidis. He made a total of 25 starts over the next three years between 1998 and 2001 for Panathinaikos and was transferred for two seasons to Iraklis before good performances led to a return to PAO in the 01/02 season. After playing second fiddle again to Nikopolidis during most of the 03/04 season, he was allowed back in to the first team after a dispute Nikopolidis had with management.
At the end of the 2003/2004 season, Nikopolidis was let out on a free transfer to bitter rivals, Olympiakos, and a new keeper was bought: Mario Galinovic. After a fight for first team football, eventually Galinovic won out and due to overseas interest, Chalkias was shipped out to English side Portsmouth F.C. in January 2005, making his debut in the FA Cup fourth round tie away at fierce rivals Southampton F.C. Unfortunately, over the next few matches Chalkias's wild tactics and inconsistency led to some poorly conceded goals, and he was soon dropped and replaced by Jamie Ashdown.
With the signing of Sander Westerveld in July 2005 Chalkias fell even further down the pecking order, and in January 2006 he was released by the club, after making only 5 appearances.
Shortly after his release from Portsmouth he joined Segunda División side Real Murcia.
Chalkias was bought in the summer transfer window of 2006 by Aris Thessaloniki. In 2008, he made the jump to cross-town rivals PAOK. He retired from football in 2012 but made a surprise comeback in 2016 by signing a contract at Panachaiki.
Chalkias was a member of the Greek national team that won the Euro 2004 in Portugal, albeit as reserve keeper and without making an appearance. In UEFA Euro 2012 tournament Chalkias made his debut on a major tournament. He ended his career als an international player after defending the goal 32 times.