This corps was composed of mountaineers, whom he himself instructed, although only one of them understood Hindustani, and his instruction had to be interpreted. The corps was armed, and expected to fight if necessary. Napier drilled them himself, and was for long his own sergeant. At a later date, when labour became plentiful, the ‘Sebundy sappers’ were disbanded. Napier lived in a log hut, and his fare was rice and sardines, varied occasionally by a jungle fowl.
In 1840 he was appointed to Sirhind, but his services at Darjiling were in such request that it was not until September 1842 that he was allowed to leave. In the meantime, on 28 Jan. 1841, he was promoted second captain. At Sirhind his duty was to lay out a cantonment to take the place of that at Karnál, which it was intended to abandon on account of its unhealthiness, and also to provide immediate accommodation for the troops then returning from Afghanistan in great numbers. Napier chose a stretch of land about four miles south of Ambala, and, impressed with the importance of the free circulation of air around dwellings as a preventive measure against sickness, he arranged the buildings in echelon on the slopes. This arrangement was freely adopted by the government in many other cantonments, and went by the name of ‘Napier's system.’
The work at Ambala was progressing when, on 15 Dec. 1845, Napier was ordered to join the army of the Satlaj under Sir Hugh (afterwards Lord) Gough [q. v.], on the outbreak of the first Sikh war. He left Ambala on horseback, and covered 150 miles in three days, arriving just in time to take command of the engineers at the battle of Mudki, where he had a horse killed under him. At the battle of Ferozeshah on 21 Dec. he again lost a horse, and, having joined the 31st regiment on foot, he was severely wounded when storming the entrenched Sikh camp. Napier was present at the battle of Sobraon on 10 Feb. 1846, no longer in command of the engineers, as officers senior to himself had joined, but he was brigade major of engineers, and accompanied the headquarter force in its advance on Lahore. Napier was mentioned in despatches, and for his services received the medal with two clasps and was promoted brevet major on 3 April 1846.
The part of the Punjab between the Bias and Satlaj rivers was annexed to the British dominion and administered by John (afterwards Lord) Lawrence [q. v.] The rest of the Punjab was ruled by Henry Lawrence, as British resident, with assistants in different parts of the country, acting with the Sikh durbár, or council of regency, on the part of the young Maharaja Dhalip Singh. This new order of things was naturally distasteful to the old Sikh soldiery of Ranjit Singh, and the garrison of the strong hill fort of Kote Kangra, 130 miles east of Lahore, determined to resist; and in May 1846 Napier served as chief engineer in the force sent under Brigadier-general Wheeler to reduce it. Napier's extraordinary energy in dragging thirty-three guns and mortars by elephants over mountain paths, and the skilful execution of the engineering work, secured the capitulation of the fort. Napier was mentioned in despatches, and received the special thanks of the government.
Napier returned for a time to Ambala and the construction of the cantonment. His charge also included the hill cantonments of Kasauli and Subáthú. He took great interest in Lawrence's asylum for children of European soldiers, which was being built at Sanáwar, near Kasauli. In October 1846 Napier selected the site of Dagshái for a new cantonment. Napier was at this time one of a group of men who were destined to be famous, and who were thrown together for some days at Subáthú and Kasauli—Henry Lawrence, Herbert Edwardes, John Becher, William Hodson, and others. On the establishment of the Lahore regency Henry Lawrence obtained for Napier the appointment of consulting engineer to the resident and council of regency of the Punjab, and Napier set to work with vigour to make roads and supervise public works.
The murder of Vans Agnew and Anderson at Multan brought on the second Sikh war in 1848, and Lieutenant (afterwards Sir) Herbert Benjamin Edwardes [q. v.] recommended that Napier should be sent to aid in the siege of Multan. The siege accordingly began under Napier's direction as chief engineer. Napier took part in the storming of the entrenched position on 9 and 12 Sept., and was wounded. The Sikh army throughout the Punjab was eager for an opportunity of a fresh trial of strength with the British. Shir Singh, who had a large body of men in the field, openly joined Diwán Mulráj, who was shut up in Multan. This made it difficult to carry on the siege without a much stronger force, and although Napier was in favour of an immediate concentrated attack, his opinion was overruled, and it was decided to await reinforcements. With the reinforcements came Colonel (afterwards Sir) John Cheape [q. v.], of the engineers, who, as senior officer, took over the direction of the siege operations. Napier was engaged in the action of Surjkund, in the capture of the suburbs, storm of the city, and surrender of the fortress