On the first day of the war, 1 September 1939, he shot down a German Henschel Hs 126. Next day, Pisarek downed - in errora Polish P-23 "Karas" bomber. On 4 September, he shot down a Ju 87 "Stuka".
After evacuation through Romania, Pisarek arrived in France.
After the French surrender, the Polish aviators flew to Oran, in French North Africa. Eventually, via Casablanca, several Polish pilots arrived in Great Britain to join the Royal Air Force.
In early August 1940, Lieutenant Marian Pisarek joined 303 "Kosciuszko" Squadron, and took part in the Battle of Britain.
On 7 September 1940, after shooting down one Messerschmitt Bf 109, he was shot down and had to bail out.
In June 1941, Pisarek was posted to command number 308 "City of Krakow" Squadron. On 14 August 1941, Pisarek claimed a Bf 109F destroyed. In April 1942, Pisarek was made Wing Commander of the 1st Polish Fighter Wing (consisting of Number 303, 316, and 317 Squadrons).
A few days later the wing was attacked over Le Touquet/Bolougne by a formation of JG 26 FW 190"son
Squadron Leader Piotr Ozyra (of 317 Sqn) and Wing Commander Pisarek were shot down and killed. Pisarek was probably shot down by the Commander of II/JG 26, Htpm.