Citation pilot reported a runway incursion after brakes failed to stop aircraft prior to runway hold short line.

Narrative

I was taxing for takeoff on [taxiway] 1 to Runway XXL as instructed by ZZZ ground. Instructions where to hold short of runway XXL and await release.Slightly prior to reaching the hold short line of XXL; I experience an intermittent brake failure. Cause unknown. After applying significant unusual pressure to the brake pedals; I was able to get the aircraft to stop. However; I had rolled past the hold short line for XXL. By the time I was able to get the plane under control; I heard the tower instruct Aircraft Y that was on short final to go around (as a result of my crossing of the hold short line).The tower then instructed me to cross runway XXL at [taxiway] 2 and contact ground. I acknowledged the instruction and crossed. [Taxiway] 2 does not have an immediate intersection across the runway to enter. [Taxiway] 3 is slightly left of the 2 entrance and 3 is slightly to the right. Not knowing which intersection to enter for the crossing on the Bravo side; I chose 3. I should have clarified which to use with the Tower; but given the adrenaline of the braking issue and the situation; I focused on 'flying the plane' first. As I taxied towards 3; I was instructed by the Tower to expedite as; 'I was on an active runway and didn't cross at 2'.I exited the runway at 3; tested my brakes again and the issue had resolved. I taxied back to XXL on 3 and departed without incident.Aircraft had recently come out of maintenance where hydraulic system had been bled for air in lines; but it shouldn't have impacted the brake any further issue.The root of the issue was the brake failure; unclear crossing instructions by the ZZZ tower and my failure to clarify the crossing instructions when the crossing exit was not clear to me.The plane had recently come out of maintenance where work was done to bleed the hydraulic lines of air. This shouldn't have impacted the braking system; but its possible that an issue may have been inadvertently caused during this maintenance event. I have the plane being inspected by mechanics now.