He was also the head coach of the Women's National Soccer League side, the NSW Sapphires, which he guided to a premiership in the 2003/04 season.

As of September 2014, Stajcic was appointed full-time head coach of the Australian women's national football team, the Matildas.

In March 2016, the Matildas qualified for the Olympic Games for the first time in 12 years, eliminating World Cup finalists Japan in the process.

Despite qualifying for the 2019 Women's World Cup, Stajcic was sacked from his position by Football Federation Australia for reasons that were not made clear by the FFA at the time of the sacking, with FFA board member Heather Reid making cryptic remarks about how people "would be shocked" if they knew the reasons, with leaks to the media resulting in Lucy Zelic claiming the facts were legally confidential.

Australian player Sam Kerr posted on Twitter saying "My trust was in Staj to lead us to the World Cup final & I believe he was the best coach for that".

[5] Heather Reid said in a statement following the settlement, "I apologise unreservedly for the damage, distress and hurt that I have caused to Alen Stajcic as a professional football coach".

[6] Following the sacking of Mike Mulvey from Central Coast Mariners, on 12 March 2019 Stajcic was appointed as the caretaker head coach for the club.

[15][16] In his guidance, he helped the team winning the 2022 AFF Women's Championship, the country's first regional trophy by blanking Thailand in the final 3-0.

[19][20] In August 2023, in the days following Philippines' exit from the Women's World Cup, Stajcic was announced as manager for Perth Glory marking his return to the A-League.

[24] His daughter Anika is a professional footballer currently playing for Perth Glory in the A-League Women competition, and has represented Australia at youth level.