Born in Košice, Lalkovič spent his early career with Košice-Barca and MFK Košice before signing for English club Chelsea in 2007. He joined Doncaster Rovers in August 2010; Lalkovič made a total of six appearances for Doncaster before returning to Chelsea. Lalkovič signed a season-long loan deal with Dutch club ADO Den Haag in August 2011, and a season-long loan deal with Portuguese club Vitória de Guimarães in July 2012. On 4 January 2013 Lalkovič was recalled by Chelsea as he was struggling to find regular playing time. On 15 July 2013, Lalkovič signed for Walsall on a six-month loan deal. During this period, Lalkovič scored 4 times in 24 appearances. On 6 January 2014, Lalkovič extended his loan with Walsall until the end of the season. On 23 May 2014, Chelsea released Lalkovič and made him available for free transfer. On 25 July 2014, Lalkovič signed a deal with Czech FK Mladá Boleslav. Following the termination of his deal with the side, he completed a free transfer to League One side Barnsley on 8 January 2015, signing an eighteen-month contract. Lalkovič made his Barnsley début coming off the bench in a 2–0 victory against Yeovil Town. Lalkovič made seventeen appearances in total for the Tykes but was permitted to conclude his contract early at the end of the season.
Walsall
Lalkovič rejoined Walsall on 16 July 2015, signing a one–year deal with the Saddlers. He scored his first goal in his second spell at Walsall in a League Cup tie against Brighton & Hove Albion.
On 28 June 2016, Lalkovič signed a two-year deal with Portsmouth for an undisclosed fee after failing to agree a new contract with Walsall. He scored his first goal for the club in a 5–1 win over Barnet on 24 September 2016. On 20 January 2017, Lalkovič joined Scottish Premiership side Ross County on loan for the remainder of the 2016–17 campaign. On transfer deadline day, Milan had his contract cancelled 6 months early by mutual consent.
On 18 October 2018, Lalkovič joined Czech First Division Side Sigma Olomouc on a short term deal until the end of the season. After the season, he left Sigma Olomouc for FC Baník Ostrava.
